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Chong ZX, Ho WY, Yeap SK. Tumour-regulatory role of long non-coding RNA HOXA-AS3. Prog Biophys Mol Biol 2024; 189:13-25. [PMID: 38593905 DOI: 10.1016/j.pbiomolbio.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Dysregulation of long non-coding RNA (lncRNA) HOXA-AS3 has been shown to contribute to the development of multiple cancer types. Several studies have presented the tumour-modulatory role or prognostic significance of this lncRNA in various kinds of cancer. Overall, HOXA-AS3 can act as a competing endogenous RNA (ceRNA) that inhibits the activity of seven microRNAs (miRNAs), including miR-29a-3p, miR-29 b-3p, miR-29c, miR-218-5p, miR-455-5p, miR-1286, and miR-4319. This relieves the downstream messenger RNA (mRNA) targets of these miRNAs from miRNA-mediated translational repression, allowing them to exert their effect in regulating cellular activities. Examples of the pathways regulated by lncRNA HOXA-AS3 and its associated downstream targets include the WNT/β-catenin and epithelial-to-mesenchymal transition (EMT) activities. Besides, HOXA-AS3 can interact with other cellular proteins like homeobox HOXA3 and HOXA6, influencing the oncogenic signaling pathways associated with these proteins. Generally, HOXA-AS3 is overexpressed in most of the discussed human cancers, making this lncRNA a potential candidate to diagnose cancer or predict the clinical outcomes of cancer patients. Hence, targeting HOXA-AS3 could be a new therapeutic approach to slowing cancer progression or as a potential biomarker and therapeutic target. A drawback of using lncRNA HOXA-AS3 as a biomarker or therapeutic target is that most of the studies that have reported the tumour-regulatory roles of lncRNA HOXA-AS3 are single observational, in vitro, or in vivo studies. More in-depth mechanistic and large-scale clinical trials must be conducted to confirm the tumour-modulatory roles of lncRNA HOXA-AS3 further. Besides, no lncRNA HOXA-AS3 inhibitor has been tested preclinically and clinically, and designing such an inhibitor is crucial as it may potentially slow cancer progression.
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Affiliation(s)
- Zhi Xiong Chong
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Wan Yong Ho
- Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia.
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia.
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Yu Q, Guo K, Yang Y, Liu H, Huang Y, Li W. LncRNA ADAMTS9-AS2 regulates periodontal ligament cell migration under mechanical compression via ADAMTS9/fibronectin. J Periodontal Res 2024; 59:174-186. [PMID: 37957805 DOI: 10.1111/jre.13204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/17/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Periodontal ligament cells (PDLCs) are key mechanosensory cells involved in extracellular matrix (ECM) remodeling during orthodontic tooth movement (OTM). Mechanical force changes the ECM components, such as collagens and matrix metalloproteinases. However, the associations between the changes in ECM molecules and cellular dynamics during OTM remain largely uncharacterized. OBJECTIVES To investigate the influence of mechanical force on the morphology and migration of PDLCs and explore the interaction between ECM remodeling and cellular dynamics, including the detailed mechanisms involved. METHODS Human PDLCs (hPDLCs) were subjected to a static mechanical compression to mimic the compression state of OTM in vitro. A mouse OTM model was used to mimic the OTM procedure in vivo. The migration of hPDLCs was compared by wound healing and transwell migration assays. Moreover, expression levels of ADAM metallopeptidase with thrombospondin type 1 motif 9 (ADAMTS9) and fibronectin (FN) in hPDLCs were determined via western blotting, immunofluorescence staining, and enzyme-linked immunosorbent assays. Expression levels of ADAMTS9 and FN in mice were assessed via immunohistochemical staining. Additionally, the relative expression of long non-coding RNA (lncRNA) ADAMTS9-antisense RNA 2 (ADAMTS9-AS2) was assessed via quantitative real-time polymerase chain reaction. ADAMTS9-AS2 knockdown was performed to confirm its function in hPDLCs. RESULTS Mechanical compression induced changes in the morphology of hPDLCs. It also promoted migration and simultaneous upregulation of FN and downregulation of ADAMTS9, a fibronectinase. The mouse OTM model showed the same expression patterns of the two proteins on the compression side of the periodontium of the moved teeth. RNA sequencing revealed that lncRNA ADAMTS9-AS2 expression was significantly upregulated in hPDLCs under mechanical compression. After knocking down ADAMTS9-AS2, hPDLCs migration was significantly inhibited. ADAMTS9 expression was increased as FN expression decreased compared to that in the control group. Moreover, knockdown of ADAMTS9-AS2 reduced the effect of mechanical compression on hPDLCs migration and reversed the expression change of ADAMTS9 and FN. RNA immunoprecipitation revealed direct binding between ADAMTS9-AS2 and ADAMTS9 protein. CONCLUSION Our study suggests that mechanical compression induces the expression of ADAMTS9-AS2, which directly binds to ADAMTS9 and inhibits its function, leading to the promotion of downstream FN expression and ECM remodeling to facilitate hPDLCs migration and maintain the stability of the periodontium.
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Affiliation(s)
- Qianyao Yu
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Kunyao Guo
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yuhui Yang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Hao Liu
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yiping Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing, China
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Hussain MS, Altamimi ASA, Afzal M, Almalki WH, Kazmi I, Alzarea SI, Saleem S, Prasher P, Oliver B, Singh SK, MacLoughlin R, Dua K, Gupta G. From carcinogenesis to therapeutic avenues: lncRNAs and mTOR crosstalk in lung cancer. Pathol Res Pract 2024; 253:155015. [PMID: 38103364 DOI: 10.1016/j.prp.2023.155015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to have a crucial function in the modulation of the activity of genes, impacting a variety of homeostatic processes involving growth, survival, movement, and genomic consistency. Certain lncRNAs' aberrant expression has been linked to carcinogenesis, tumor growth, and therapeutic resistance. They are beneficial for the management of malignancies since they can function as cancer-causing or cancer-suppressing genes and behave as screening or prognosis indicators. The modulation of the tumor microenvironment, metabolic modification, and spread have all been linked to lncRNAs in lung cancer. Recent research has indicated that lncRNAs may interact with various mTOR signalling systems to control expression in lung cancer. Furthermore, the route can affect how lncRNAs are expressed. Emphasizing the function of lncRNAs as crucial participants in the mTOR pathway, the current review intends to examine the interactions between the mTOR cascade and the advancement of lung cancer. The article will shed light on the roles and processes of a few lncRNAs associated with the development of lung cancer, as well as their therapeutic prospects.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | - Abdulmalik S A Altamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- ōDepartment of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Energy Acres, Dehradun 248007, India
| | - Brian Oliver
- Faculty of Science, School of Life Sciences, Sydney, NSW 2007, Australia; Woolcock Institute of Medical Research, Macquarie university, Sydney, NSW, 2137
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ronan MacLoughlin
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster D02 YN77, Ireland; School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster D02 PN40, Ireland; Research and Development, Science and Emerging Technologies, Aerogen Ltd., Galway Business Park, H91 HE94 Galway, Ireland
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India; School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India.
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Ao YQ, Gao J, Jiang JH, Wang HK, Wang S, Ding JY. Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village. Mol Ther 2023; 31:3389-3413. [PMID: 37740493 PMCID: PMC10727995 DOI: 10.1016/j.ymthe.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.
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Affiliation(s)
- Yong-Qiang Ao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jian-Yong Ding
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.
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Wang J, Xia B, Ma R, Ye Q. Comprehensive Analysis of a Competing Endogenous RNA Co-Expression Network in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2023; 18:2417-2429. [PMID: 37955025 PMCID: PMC10637225 DOI: 10.2147/copd.s431041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is the main cause of mortality world widely. Non-coding RNAs (lncRNAs) and associated competitive endogenous RNAs (ceRNAs) networks were recently proved to lead to mRNA gene expression downregulation but were still unclear in COPD. This study aims to investigate and elucidate the mechanisms underlying the involvement of ceRNA co-expression networks in COPD pathogenesis. Methods Obtained expression signature of data from the Gene Expression Omnibus database and compared the differentially expression of mRNAs and miRNAs between COPD patients and healthy smokers. Predicted the miRNA-lncRNA and miRNA-mRNA interaction using online library and employed CIBERSORT to measure the proportions of the 22 immune cells in the COPD and control groups. Results Established a ceRNA-network comprising 11 lncRNAs, 5 miRNAs, and 16 mRNAs. Using the weighted correlation network analysis method, we identified hub genes and hub miRNAs and obtained one core sub-network, XIST, FGD5-AS1, KCNQ1OT1, HOXA11-AS, LINC00667, H19, PRKCQ-AS1, NUTM2A-AS1/has-mir-454-3p/ZNF678, PRRG4. COPD patients had different proportions of immune cells than controls, and these variations were associated with the magnitude of pulmonary function parameters. Conclusion The ceRNA-network, particularly the core sub-network, may be a putative goal for COPD, in which specific immune cells were involved.
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Affiliation(s)
- Jingwei Wang
- Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Bowen Xia
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Ruimin Ma
- Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Qiao Ye
- Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China
- Department of Occupational Medicine and Toxicology, Clinical Center for Interstitial Lung Diseases, Beijing Chaoyang Hospital, Capital Medical University, Beijing, People’s Republic of China
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Garbo E, Del Rio B, Ferrari G, Cani M, Napoli VM, Bertaglia V, Capelletto E, Rolfo C, Novello S, Passiglia F. Exploring the Potential of Non-Coding RNAs as Liquid Biopsy Biomarkers for Lung Cancer Screening: A Literature Review. Cancers (Basel) 2023; 15:4774. [PMID: 37835468 PMCID: PMC10571819 DOI: 10.3390/cancers15194774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Lung cancer represent the leading cause of cancer mortality, so several efforts have been focused on the development of a screening program. To address the issue of high overdiagnosis and false positive rates associated to LDCT-based screening, there is a need for new diagnostic biomarkers, with liquid biopsy ncRNAs detection emerging as a promising approach. In this scenario, this work provides an updated summary of the literature evidence about the role of non-coding RNAs in lung cancer screening. A literature search on PubMed was performed including studies which investigated liquid biopsy non-coding RNAs biomarker lung cancer patients and a control cohort. Micro RNAs were the most widely studied biomarkers in this setting but some preliminary evidence was found also for other non-coding RNAs, suggesting that a multi-biomarker based liquid biopsy approach could enhance their efficacy in the screening context. However, further studies are needed in order to optimize detection techniques as well as diagnostic accuracy before introducing novel biomarkers in the early diagnosis setting.
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Affiliation(s)
- Edoardo Garbo
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Benedetta Del Rio
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Giorgia Ferrari
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Massimiliano Cani
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Valerio Maria Napoli
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Valentina Bertaglia
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Enrica Capelletto
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
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Akhgari H, Shokri N, Dehghanzadeh P, Tayefeh-Gholami S, Rajabi A, Safaralizadeh R. Expression pattern of PCAT1, PCAT2, and PCAT5 lncRNAs and their value as diagnostic biomarkers in patients with gastric cancer. Pathol Res Pract 2023; 248:154654. [PMID: 37392552 DOI: 10.1016/j.prp.2023.154654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/04/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Gastric cancer (GC), is a complex multifactorial neoplasm with a high mortality and prevalence rate all over the world. Hence, it is necessary to identify the multiple pathways that are previously unknown and are involved in its initiation and progression. Recently, it has become clear that long non-coding RNAs (lncRNAs) play a crucial role in the onset and spread of cancer. The current study assessed the lncRNAs PCAT1, PCAT2, and PCAT5 expression in primary gastric tumors and adjacent noncancerous tissues. METHODS 90 pairs of GC and adjacent noncancerous tissue samples were obtained. Total RNA was extracted, then cDNA was synthesized. Using quantitative reverse transcriptase PCR (qRT-PCR), PCAT1, PCAT2, and PCAT5 expression levels were evaluated. Using the SPSS statistical package, the correlation between clinicopathological characteristics and the expression of PCAT1, PCAT2, and PCAT5 was investigated. The diagnostic value of PCAT1, PCAT2, and PCAT5 in GC was assessed using the receiver operating characteristic (ROC) curve analysis. RESULTS Compared to surrounding non-cancerous tissues, PCAT1, PCAT2, and PCAT5 were all significantly overexpressed in tumoral tissues (P = 0.001, P = 0.019, and P = 0.0001, respectively). PCAT5 expression was significantly associated with gender (P = 0.020), according to our research. The ROC curve's findings indicated that PCAT1, PCAT2, and PCAT5 may each function as poor diagnostic biomarkers, with respective AUC values of 64 %, 60 %, and 68 %, specificity values of 68 %, 60 %, and 76 %, and sensitivity values of 55 %, 72 %, and 52 %. CONCLUSION Our research suggested that PCAT1, PCAT2, and PCAT5 may be engaged in promoting and developing GC cells as a novel oncogene because of the increased expression of PCAT1, PCAT2 and PCAT5 in tumor tissues of GC patients. Additionally, PCAT1, PCAT2, and PCAT5 can be thought of as poor diagnostic biomarkers for GC case detection.
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Affiliation(s)
- Hossein Akhgari
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Neda Shokri
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Parisa Dehghanzadeh
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Samaneh Tayefeh-Gholami
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Ali Rajabi
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Departmant of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
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Yang H, Chen Y, Zeng M, Wu H, Zou X, Fang T, Zhai L, Liang H, Luo H, Tian G, Liu Q, Tang H. Long non-coding RNA LINC01480 is activated by Foxo3a and promotes hydroquinone-induced TK6 cell apoptosis by inhibiting the PI3K/AKT pathway. Ecotoxicol Environ Saf 2023; 255:114786. [PMID: 36934544 DOI: 10.1016/j.ecoenv.2023.114786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/04/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a critical role in the damage caused to the body by environmental exogenous chemicals; however, few studies have explored their effects during exposure to benzene and its metabolite, hydroquinone (HQ). An emerging lncRNA, LINC01480, was found to be associated with the immune microenvironment of some cancers, but its specific function remains unknown. Therefore, this study aimed to investigate the role of LINC01480 in HQ-induced apoptosis. The biological function of LINC01480 was investigated through gain-of-function and loss-of-function experiments. Mechanically, nuclear-cytoplasmic fractionation experiment, chromatin immunoprecipitation (ChIP), dual-luciferase reporter assay, and rescue experiments were performed. In this study, when TK6 cells were treated with HQ (0, 5, 10, and 20 μM) for 12, 24, 48, and 72 h, the expression of LINC01480 was increased in a dose-dependent manner. Meanwhile, the phosphorylation levels of PI3K and AKT decreased, and apoptosis increased. As compared to the control group, HQ-induced apoptosis was significantly reduced, and the relative survival rate of TK6 cells increased after silencing LINC01480, while overexpression of LINC01480 further sensitized TK6 cells to HQ-induced apoptotic cell death. LINC01480 negatively regulated the PI3K/AKT pathway in TK6 cells, and the apoptosis-inhibiting effect of LINC01480 silencing was reversed after inhibition of the PI3K/AKT pathway. In addition, ChIP and the dual-luciferase reporter assays showed that the transcription factor Foxo3a promoted LINC01480 transcription by directly binding to the promoter regions - 149 to - 138 of LINC01480. Moreover, short-term HQ exposure promoted the expression of Foxo3a. From these findings, we can conclude that LINC01480 is activated by Foxo3a, and promotes HQ-induced apoptosis by inhibiting the PI3K/AKT pathway, suggesting that LINC01480 might become a possible target for therapeutic intervention of HQ-induced toxicity.
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Affiliation(s)
- Hui Yang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Yuting Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Minjuan Zeng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Haipeng Wu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Xiangli Zou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Tiantian Fang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Lu Zhai
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Hairong Liang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Hao Luo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Gaiqin Tian
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China
| | - Qizhan Liu
- Center for Global Health, The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Huanwen Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, Guangdong, China; Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan 523808, Guangdong, China.
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Yalimaimaiti S, Liang X, Zhao H, Dou H, Liu W, Yang Y, Ning L. Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs. BMC Bioinformatics 2023; 24:81. [PMID: 36879187 PMCID: PMC9990240 DOI: 10.1186/s12859-023-05192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE To establish a prognostic signature for lung adenocarcinoma (LUAD) based on cuproptosis-related long non-coding RNAs (lncRNAs), and to study the immune-related functions of LUAD. METHODS First, transcriptome data and clinical data related to LUAD were downloaded from the Cancer Genome Atlas (TCGA), and cuproptosis-related genes were analyzed to identify cuproptosis-related lncRNAs. Univariate COX analysis, least absolute shrinkage and selection operator (LASSO) analysis, and multivariate COX analysis were performed to analyze the cuproptosis-related lncRNAs, and a prognostic signature was established. Second, univariate COX analysis and multivariate COX analysis were performed for independent prognostic analyses. Receiver operating characteristic (ROC) curves, C index, survival curve, nomogram, and principal component analysis (PCA) were performed to evaluate the results of the independent prognostic analyses. Finally, gene enrichment analyses and immune-related function analyses were also carried out. RESULTS (1) A total of 1,297 cuproptosis-related lncRNAs were screened. (2) A LUAD prognostic signature containing 13 cuproptosis-related lncRNAs was constructed (NIFK-AS1, AC026355.2, SEPSECS-AS1, AL360270.1, AC010999.2, ABCA9-AS1, AC032011.1, AL162632.3, LINC02518, LINC0059, AL031600.2, AP000346.1, AC012409.4). (3) The area under the multi-indicator ROC curves at 1, 3, and 5 years were AUC1 = 0.742, AUC2 = 0.708, and AUC3 = 0.762, respectively. The risk score of the prognostic signature could be used as an independent prognostic factor that was independent of other clinical indicators. (4) The results of gene enrichment analyses showed that 13 biomarkers were primarily related to amoebiasis, the wnt signaling pathway, hematopoietic cell lineage. The ssGSEA volcano map showed significant differences between high- and low-risk groups in immune-related functions, such as human leukocyte antigen (HLA), Type_II_IFN_Reponse, MHC_class_I, and Parainflammation (P < 0.001). CONCLUSIONS Thirteen cuproptosis-related lncRNAs may be clinical molecular biomarkers for the prognosis of LUAD.
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Affiliation(s)
- Saiyidan Yalimaimaiti
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Xiaoqiao Liang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Haili Zhao
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Hong Dou
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Wei Liu
- Xinjiang Uygur Autonomous Region Occupational Disease Hospital, Urumqi, 830011, Xinjiang, China
| | - Ying Yang
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Li Ning
- School of Public Health, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
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Ghafouri-Fard S, Askari A, Hussen BM, Baniahmad A, Taheri M, Mokhtari M. A review on the role of ADAMTS9-AS2 in different disorders. Pathol Res Pract 2023; 243:154346. [PMID: 36746036 DOI: 10.1016/j.prp.2023.154346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recent decade has seen a tremendous progress in identification of the role of different long non-coding RNAs (lncRNAs) in human pathologies. ADAMTS9-AS2 is an example of lncRNAs with different roles in human disorders. It is mostly acknowledged as a tumor suppressor lncRNA in different types of cancers. However, it has been reported to be up-regulated in tongue squamous cell carcinoma, salivary adenoid cystic carcinoma and glioblastoma. Moreover, ADAMTS9-AS2 is possibly involved in the pathoetiology of pulpitis, acute ischemic stroke, type 2 diabetes and its complications. This lncRNA sponges miR-196b-5p, miR-223-3p, miR-130a-5p, miR-600, miR-223-3p, miR-27a-3p, miR-32, miR-143-3p, miR-143-3p and miR-182-5p in order to regulate downstream mRNAs. This review aims at summarization of the role of ADAMTS9-AS2 in different disorders with a particular focus on its diagnostic and prognostic values.
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Long J, Liu L, Yang X, Zhou X, Lu X, Qin L. LncRNA NUTM2A-AS1 aggravates the progression of hepatocellular carcinoma by activating the miR-186-5p/KLF7-mediated Wnt/beta-catenin pathway. Hum Cell 2023; 36:312-328. [PMID: 36242728 DOI: 10.1007/s13577-022-00802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 09/28/2022] [Indexed: 01/20/2023]
Abstract
Emerging evidence has uncovered that noncoding RNAs (ncRNAs) contribute to the development of hepatocellular carcinoma (HCC). Nevertheless, the functions of the majority of long ncRNAs (lncRNAs) in HCC are unknown. Here, we intend to probe the function of lncRNA NUTM2A-AS1 in the evolvement of HCC and the related mechanism. Expression levels of lncRNA NUTM2A-AS1, miR-186-5p and KLF7 mRNA in HCC tissues and adjacent non-tumor tissues were monitored. Gain- or loss-of-function assays were utilized to investigate the biological functions of lncRNA NUTM2A-AS1, miR-186-5p and KLF7 in HCC cell lines (including HCCLM3 and Huh7). Western blot was implemented for the detection of the epithelial-mesenchymal transition (EMT)-related proteins (including E-cadherin, Vimentin and Snail), KLF7, Wnt, β-catenin, and stemness-related proteins (Nanog, OCT4, YKL40, and CD133). Furthermore, the targeted associations between lncRNA NUTM2A-AS1, miR-186-5p, and KLF7 were verified by bioinformatics analysis, dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. As a result, lncRNA NUTM2A-AS1 and KLF7 profiles were heightened in the HCC tissues versus adjacent normal tissues, while miR-186-5p had the opposite expression tendency. Up-regulation of lncRNA NUTM2A-AS1 was related to tumor size, advanced tumor stage, and lymph node metastasis of HCC patients. Functionally, overexpression of lncRNA NUTM2A-AS1 heightened HCC cells' growth, invasion, EMT, and stemness and repressed their apoptosis by activating the Wnt/β-catenin pathway. In contrast, up-regulation of miR-186-5p or inhibition of KLF7 had reverse effects. In vivo, lncRNA NUTM2A-AS1 overexpression facilitated tumor growth and EMT, accompanied by declined miR-186-5p levels and enhanced KLF7 expression. The mechanistic studies revealed that miR-186-5p served as a common target of lncRNA NUTM2A-AS1 and KLF7. As hinted by the rescue experiments, NUTM2A-AS1 partly abated miR-186-5p-mediated anti-tumor effects in HCC cells, whereas KLF7 knockdown reversed the promotive effects of NUTM2A-AS1. LncRNA NUTM2A-AS1 accelerated the evolution of HCC by up-regulating the KLF7/Wnt/beta-catenin pathway through sponging miR-186-5p.
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Affiliation(s)
- Jianwu Long
- Department of Hepatobiliary Surgery, Hengyang Medical School, The Affiliated Nanhua Hospital, University of South China, No. 336, Dongfeng South Road, Zhuhui District, Hengyang City, 421000, China.,Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 899 Pinghai Road, Gusu District, Suzhou City, 215000, Jiangsu, China
| | - Longfei Liu
- Department of Hepatobiliary Surgery, Hengyang Medical School, The Affiliated Nanhua Hospital, University of South China, No. 336, Dongfeng South Road, Zhuhui District, Hengyang City, 421000, China
| | - Xuefeng Yang
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Xiaojun Zhou
- Department of Hepatobiliary Surgery, Hengyang Medical School, The Affiliated Nanhua Hospital, University of South China, No. 336, Dongfeng South Road, Zhuhui District, Hengyang City, 421000, China
| | - Xianzhou Lu
- Department of Hepatobiliary Surgery, Hengyang Medical School, The Affiliated Nanhua Hospital, University of South China, No. 336, Dongfeng South Road, Zhuhui District, Hengyang City, 421000, China.
| | - Lei Qin
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No. 899 Pinghai Road, Gusu District, Suzhou City, 215000, Jiangsu, China.
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Pan H, Peng J, Qiao X, Gao H. Upregulation of lncRNA LANCL1-AS1 inhibits the progression of non-small-cell lung cancer via the miR-3680-3p/GMFG axis. Open Med (Wars) 2023; 18:20230666. [PMID: 36941990 PMCID: PMC10024345 DOI: 10.1515/med-2023-0666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 03/18/2023] Open
Abstract
Patients with non-small-cell lung cancer (NSCLC) have a low survival rate. Long non-coding RNA (LncRNA) LANCL1 antisense RNA 1 (LANCL1-AS1) was indicated to be downregulated in NSCLC; however, its detailed function in NSCLC is unanswered. Real-time quantitative polymerase chain reaction revealed the downregulation of LANCL1-AS1 in NSCLC cell lines and subcellular fractionation assay showed that LANCL1-AS1 was mainly located in the cytoplasm of NSCLC cells. Cell counting kit-8, Transwell, and tube formation assays displayed that overexpression of LANCL1-AS1 suppressed NSCLC cell proliferation, migration, invasiveness, and angiogenesis in vitro. Animal experiments validated the tumor-suppressive role of LANCL1-AS1 in tumor-bearing mice. Mechanistically, LANCL1-AS1 upregulated glia maturation factor gamma (GMFG) expression by competitively binding to miR-3680-3p. GMFG knockdown reversed LANCL1-AS1 overexpression-mediated inhibitory impact on NSCLC malignant behaviors. Collectively, LANCL1-AS1 upregulation inhibits the progression of NSCLC by modulating the miR-3680-3p/GMFG axis.
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Affiliation(s)
- Hui Pan
- Department of Respiratory Medicine, Gansu Provincial Hospital, Lanzhou730000, Gansu, China
| | - Jing Peng
- Department of Customer Service Center, Gansu Provincial Hospital, Lanzhou730000, Gansu, China
| | - Xiaoni Qiao
- Department of Information Center, Gansu Provincial Hospital, Lanzhou730000, Gansu, China
| | - Han Gao
- Department of Information Center, Gansu Provincial Hospital, Lanzhou730000, Gansu, China
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Mao W, Liao Y, Tang L. Long Intergenic Non-Protein Coding RNA 173 in Human Cancers. Cancers (Basel) 2022; 14. [PMID: 36497407 DOI: 10.3390/cancers14235923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Long non-coding RNAs belong to non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides and limited protein-coding ability. Growing research has clarified that dysregulated lncRNAs are correlated with the development of various complex diseases, including cancer. LINC00173 has drawn researchers' attention as one of the recently discovered lncRNAs. Aberrant expression of LINC00173 affects the initiation and progression of human cancers. In the present review, we summarize the recent considerable research on LINC00173 in 11 human cancers. Through the summary of the abnormal expression of LINC00173 and its potential molecular regulation mechanism in cancers, this article indicates that LINC00173 may serve as a potential diagnostic biomarker and a target for drug therapy, thus providing novel clues for future related research.
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Li Y, Chen C, Liu HL, Zhang ZF, Wang CL. LARRPM restricts lung adenocarcinoma progression and M2 macrophage polarization through epigenetically regulating LINC00240 and CSF1. Cell Mol Biol Lett 2022; 27:91. [PMID: 36221069 PMCID: PMC9552444 DOI: 10.1186/s11658-022-00376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are critical regulators in lung adenocarcinoma (LUAD). M2-type tumor-associated macrophages (TAMs) also play oncogenic roles in LUAD. However, the involvement of lncRNAs in TAM activation is still largely unknown. METHODS The expressions of LARRPM, LINC00240 and CSF1 were determined by RT-qPCR. The regulation of LINC00240 and CSF1 by LARRPM was investigated by RNA-protein pull-down, RNA immunoprecipitation, chromatin immunoprecipitation and bisulfite DNA sequencing. In vitro and in vivo gain- and loss-of-function assays were performed to investigate the roles of LARRPM. RESULTS The lncRNA LARRPM was expressed at low levels in LUAD tissues and cells. The low expression of LARRPM was correlated with advanced stage and poor survival of patients with LUAD. Functional experiments revealed that LARRPM suppressed LUAD cell proliferation, migration and invasion, and promoted apoptosis. LARRPM also repressed macrophage M2 polarization and infiltration. Taken together, LARRPM significantly restricted LUAD progression in vivo. Mechanistically, LARRPM bound and recruited DNA demethylase TET1 to the promoter of its anti-sense strand gene LINC00240, leading to a decrease in DNA methylation level of the LINC00240 promoter and transcriptional activation of LINC00240. Functional rescue assays suggested that the lncRNA LINC00240 was responsible for the roles of LARRPM in the malignant behavior of LUAD cells. LARRPM decreased the binding of TET1 to the CSF1 promoter, resulting in increased DNA methylation of the CSF1 promoter and transcriptional repression of CSF1, which is responsible for the roles of LARRPM in macrophage M2 polarization and infiltration. The TAMs educated by LUAD cells exerted oncogenic roles, which was negatively regulated by LARRPM expressed in LUAD cells. CONCLUSIONS LARRPM restricts LUAD progression through repressing both LUAD cell and macrophages. These data shed new insights into the regulation of LUAD progression by lncRNAs and provide data on the potential utility of LARRPM as a target for LUAD treatment.
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Affiliation(s)
- Yue Li
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Chen Chen
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Hai-Lin Liu
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Zhen-Fa Zhang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China
| | - Chang-Li Wang
- Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Lung Cancer Center, Tianjin, 300060, China.
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Wang Y, Lu G, Xue X, Xie M, Wang Z, Ma Z, Feng Y, Shao C, Duan H, Pan M, Ding P, Li X, Han J, Yan X. Characterization and validation of a ferroptosis-related LncRNA signature as a novel prognostic model for lung adenocarcinoma in tumor microenvironment. Front Immunol 2022; 13:903758. [PMID: 36016939 PMCID: PMC9395983 DOI: 10.3389/fimmu.2022.903758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022] Open
Abstract
Ferroptosis is a more relatively recently identified type of programmed cell death, which is associated with tumor progression. However, the mechanism underlying the effect of ferroptosis-related long non-coding RNAs (lncRNAs) in lung adenocarcinoma (LUAD) remains elusive. Therefore, the current study aimed to investigate the role of ferroptosis-related lncRNAs in LUAD and to develop a prognostic model. The clinicopathological characteristics of patients and the gene sequencing data were obtained from The Cancer Genome Atlas, while the ferroptosis-associated mRNAs were downloaded from the FerrDb database. A ferroptosis-related lncRNA signature was established with Least Absolute Shrinkage and Selection Operator Cox regression analysis. Furthermore, the risk scores of ferroptosis-related lncRNAs were calculated and LUAD patients were then assigned to high- and low-risk groups based on the median risk score. The prognostic model was established by K-M plotters and nomograms. Gene set enrichment analysis (GSEA) was performed to evaluate the association between immune responses and ferroptosis-related lncRNAs. A total of 10 ferroptosis-related lncRNAs were identified as independent predictors of LUAD outcome, namely RP11-386M24.3, LINC00592, FENDRR, AC104699.1, AC091132.1, LANCL1-AS1, LINC-PINT, IFNG-AS1, LINC00968 and AC006129.2. The area under the curve verified that the established signatures could determine LUAD prognosis. The nomogram model was used to assess the predictive accuracy of the established signatures. Additionally, GSEA revealed that the 10 ferroptosis-related lncRNAs could be involved in immune responses in LUAD. Overall, the results of the current study may provide novel insights into the development of novel therapies or diagnostic strategies for LUAD.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Guofang Lu
- Department of Physiology and Pathophysiology, National Key Discipline of Cell Biology, Fourth Military Medical University, Xi’an, China
- State Key Laboratory of Cancer Biology and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, China
| | - Xinying Xue
- Department of Respiratory Disease, Beijing Shijitan Hospital, Capital Medical University, Peking University Ninth School of Clinical Medicine, Beijing, China
- Department of Respiratory Disease, School of Clinical Medicine, Weifang Medical University, Weifang, China
- Department of Respiratory and Critical Care, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Mei Xie
- Department of Respiratory and Critical Care, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhaoyang Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Zhiqiang Ma
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yingtong Feng
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Changjian Shao
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Hongtao Duan
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Minghong Pan
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Peng Ding
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Xiaofei Li
- Department of Thoracic Surgery, Xi’an International Medical Center Hospital, Xi’an, China
- *Correspondence: Xiaolong Yan, ; Jing Han, hanjing.cn.@163.com; Xiaofei Li,
| | - Jing Han
- Department of Ophthalmology, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
- *Correspondence: Xiaolong Yan, ; Jing Han, hanjing.cn.@163.com; Xiaofei Li,
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
- *Correspondence: Xiaolong Yan, ; Jing Han, hanjing.cn.@163.com; Xiaofei Li,
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Wang J, Liang H, Zhang Q, Ma S. Replicability in cancer omics data analysis: measures and empirical explorations. Brief Bioinform 2022; 23:6649493. [PMID: 35876281 PMCID: PMC9487717 DOI: 10.1093/bib/bbac304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 02/05/2023] Open
Abstract
In biomedical research, the replicability of findings across studies is highly desired. In this study, we focus on cancer omics data, for which the examination of replicability has been mostly focused on important omics variables identified in different studies. In published literature, although there have been extensive attention and ad hoc discussions, there is insufficient quantitative research looking into replicability measures and their properties. The goal of this study is to fill this important knowledge gap. In particular, we consider three sensible replicability measures, for which we examine distributional properties and develop a way of making inference. Applying them to three The Cancer Genome Atlas (TCGA) datasets reveals in general low replicability and significant across-data variations. To further comprehend such findings, we resort to simulation, which confirms the validity of the findings with the TCGA data and further informs the dependence of replicability on signal level (or equivalently sample size). Overall, this study can advance our understanding of replicability for cancer omics and other studies that have identification as a key goal.
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Affiliation(s)
- Jiping Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Hongmin Liang
- Department of Statistics, School of Economics, Xiamen University, Xiamen, Fujian, China
| | - Qingzhao Zhang
- Department of Statistics, School of Economics, Xiamen University, Xiamen, Fujian, China,The Wang Yanan Institute for Studies in Economics, Xiamen University, Xiamen, Fujian, China
| | - Shuangge Ma
- Corresponding author. Shuangge Ma, Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA. Tel.: +1-203-785-3119; Fax: +1-203-785-6912; E-mail:
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Pan T, Wang H, Wang S, Liu F. Long Non-Coding RNA LINC01929 Facilitates Cell Proliferation and Metastasis as a Competing Endogenous RNA Against MicroRNA miR-1179 in Non-Small Cell Lung Carcinoma. Br J Biomed Sci 2022; 79:10598. [PMID: 35996496 PMCID: PMC9329516 DOI: 10.3389/bjbs.2022.10598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022]
Abstract
Introduction: Non-small cell lung carcinoma (NSCLC) constitutes most lung cancers and has a poor prognosis. LncRNAs are a potential repository for the discovery of cancer prognostic markers. This study explored the role of LINC01929 in NSCLC, both the clinical prognostic significance and the mechanism of its influence on cells. Materials and Methods: LINC01929 levels in 143 pairs of NSCLC tissues and non-cancerous tissues were detected by RT-qPCR. Kaplan-Meier curves and multivariate Cox regression assays were generated for evaluating the prognostic values of LINC01929. To evaluate the cellular function, an XTT assay and transwell invasion assays were performed. Results: LINC01929 was up-regulated in NSCLC tissues compared with healthy tissues. A positive correlation was observed between LINC01929 expression level and tumor T (p = 0.002) or N stage (p = 0.010). Patients with higher LINC01929 levels had shorter overall survival (p = 0.009). Compared with other factors, high LINC01929 expression was significantly associated with poor survival in univariate Cox analysis (HR: 2.485, 95%CI: 1.220–5.060, p = 0.012). After multivariate Cox regression assays, LINC01929 was a independent prognostic factor (HR: 3.021, 95%CI: 1.377–6.628, p = 0.006). miR-1179 was a target miRNA of LINC01929. Inhibited expression of LINC01929 significantly reduced the proliferation, migration, and invasion of NSCLC cells by targeting miR-1179. Discussion: This study revealed the upregulation of LINC01929 in NSCLC. This study supports previous studies showing LINC01929 as a potential prognostic factor for NSCLC.
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Affiliation(s)
- Tinghong Pan
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Hui Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Shuai Wang
- Department of Thoracic Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Feng Liu
- Department of Cardiothoracic Surgery, Zhucheng People’s Hospital, Weifang, China
- *Correspondence: Feng Liu, , orcid.org/0000-0002-3218-9173
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Ying H, Jin Y, Guo Y, Li Q, Ruan M, Zhu W, Yang C, Li Q, Zheng L. Long non-coding RNA NUT family member 2A-antisense RNA 1 sponges microRNA-613 to increase the resistance of gastric cancer cells to matrine through regulating oxidative stress and vascular endothelial growth factor A. Aging (Albany NY) 2022; 14:5153-62. [PMID: 35771149 DOI: 10.18632/aging.204135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Matrine has been shown to play a role in the suppression of gastric cancer (GC) tumorigenesis. However, whether long non-coding RNA NUT family member 2A-antisense RNA 1 (NUTM2A-AS1) is involved in matrine-induced inhibition of GC remains unknown. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, cell colony formation, and terminal deoxynucleotidyl transferase dUTP nick-end labeling assays were employed to determine the proliferation, viability, and apoptosis of GC cells, respectively. The Cancer Genome Atlas database suggested an association between NUTM2A-AS1 and GC. The reverse transcription-quantitative polymerase chain reaction was used to quantify relative levels of NUTM2A-AS1, miR-613, and vascular endothelial growth factor A (VEGFA). Reactive oxygen species generation, glutathione content, and superoxide dismutase activity were determined by corresponding reagents or assay kits. NUTM2A-AS1 knockdown led to attenuated cell viability and proliferation, as well as to enhanced apoptosis of N87 and AGS cells treated with matrine. These changes were prevented by an inhibitor of microRNA (miR)-613. Importantly, NUTM2A-AS1 expression was positively associated with tumor progression in patients with GC. NUTM2A-AS1 and miR-613 regulated the generation of reactive oxygen species, the content of glutathione, and the activity of superoxide dismutase. VEGFA served as an important effector for the NUTM2A-AS1/miR-613-regulated resistance of GC cells to matrine. These results reveal a novel mechanism of matrine resistance in GC.
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Wang Y, Liu F, Chen L, Fang C, Li S, Yuan S, Qian X, Yin Y, Yu B, Fu B, Zhang X, Li Y. Neutrophil Extracellular Traps (NETs) Promote Non-Small Cell Lung Cancer Metastasis by Suppressing lncRNA MIR503HG to Activate the NF-κB/NLRP3 Inflammasome Pathway. Front Immunol 2022; 13:867516. [PMID: 35707534 PMCID: PMC9190762 DOI: 10.3389/fimmu.2022.867516] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/02/2022] [Indexed: 12/20/2022] Open
Abstract
Neutrophil extracellular traps (NETs) that are produced in the tumour microenvironment (TME) have been suggested to play an essential role in the dissemination of metastatic cancer under multiple infectious and inflammatory conditions. However, the functions of NETs in promoting non-small cell lung cancer (NSCLC) metastasis and the underlying mechanisms remain incompletely understood. Here, we found that NETs promoted NSCLC cell invasion and migration by inducing epithelial to mesenchymal transition (EMT). To explore how NETs contribute to NSCLC metastasis, microarrays were performed to identify substantial numbers of long noncoding RNAs (lncRNAs) and mRNAs that were differentially expressed in NSCLC cells after stimulation with NETs. Interestingly, we observed that the expression of lncRNA MIR503HG was downregulated after NETs stimulation, and ectopic MIR503HG expression reversed the metastasis-promoting effect of NETs in vitro and in vivo. Notably, bioinformatics analysis revealed that differentially expressed genes were involved in the NOD-like receptor and NF-κB signalling pathways that are associated with inflammation. NETs facilitated EMT and thereby contributed to NSCLC metastasis by activating the NF-κB/NOD-like receptor protein 3 (NLRP3) signalling pathway. Further studies revealed that MIR503HG inhibited NETs-triggered NSCLC cell metastasis in an NF-κB/NLRP3-dependent manner, as overexpression of NF-κB or NLRP3 impaired the suppressive effect of MIR503HG on NETs-induced cancer cell metastasis. Together, these results show that NETs activate the NF-κB/NLRP3 pathway by downregulating MIR503HG expression to promote EMT and NSCLC metastasis. Targeting the formation of NETs may be a novel therapeutic strategy for treating NSCLC metastasis.
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Affiliation(s)
- Yong Wang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fen Liu
- Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lin Chen
- Department of Internal Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Fang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuangyan Li
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shangkun Yuan
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoying Qian
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yan Yin
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Biao Yu
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Biqi Fu
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinwei Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yong Li
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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20
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Li Y, Li J, Chen H, Wang J, Jiang L, Tan X. The lncARSR/PTEN/Akt/nuclear factor-kappa B feedback regulatory loop contributes to doxorubicin resistance in hepatocellular carcinoma. J Biochem Mol Toxicol 2022; 36:e23119. [PMID: 35678308 DOI: 10.1002/jbt.23119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/25/2022] [Accepted: 05/29/2022] [Indexed: 11/07/2022]
Abstract
Chemoresistance is a major obstacle to hepatocellular carcinoma (HCC) chemotherapy. Our previous study found that long noncoding RNA lncARSR (lncRNA Activated in RCC with Sunitinib Resistance) activated Akt signaling via repressing phosphatase and tensin homolog (PTEN) during doxorubicin resistance in HCC. The purpose of this study is to further explore lncARSR-mediated mechanisms and roles during doxorubicin resistance in HCC. The expression of lncARSR was detected by real-time quantitative polymerase chain reaction (qPCR). Nuclear factor-kappa B (NF-κB) activity was detected by NF-κB luciferase reporter assays, western blot, and NF-κB transcription factor assays. The effects of NF-κB on lncARSR were detected by chromatin immunoprecipitation assay, promoter luciferase reporter assay, and real-time qPCR. The effects of lncARSR/Akt/NF-κB on doxorubicin resistance were detected by Cell Counting Kit-8 assay, capsase-3 activity assay, and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling assay. lncARSR activated NF-κB signaling through activation of Akt. NF-κB transactivated lncARSR through directly binding lncARSR promoter and increasing lncARSR promoter activity. Akt transactivated lncARSR via activating NF-κB signaling. Thus, lncARSR, Akt, and NF-κB formed a positive feedback regulatory loop in HCC. Through this feedback loop, lncARSR auto-regulated its transcription. Drug sensitivity assays showed that the lncARSR/Akt/NF-κB feedback regulatory loop promoted doxorubicin resistance in HCC. These findings identified the lncARSR/Akt/NF-κB feedback regulatory loop in HCC, which represent potential therapeutic targets for improving doxorubicin sensitivity in HCC.
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Affiliation(s)
- Yaling Li
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jun Li
- Department of Anorectal, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Hongyan Chen
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jiting Wang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.,Department of Clinical Pharmacy, School of Pharmacy, Southwest Medical University, Sichuan, China
| | - Linhan Jiang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.,Department of Clinical Pharmacy, School of Pharmacy, Southwest Medical University, Sichuan, China
| | - Xiaoxia Tan
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.,Department of Clinical Pharmacy, School of Pharmacy, Southwest Medical University, Sichuan, China
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21
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Zhang S, Jiang M, Cao H, Xiong J, Xu J. CTB-193M12.5 Promotes Hepatocellular Carcinoma Progression via Enhancing NSD1-Mediated WNT10B/Wnt/β-Catenin Signaling Activation. J Hepatocell Carcinoma 2022; 9:553-569. [PMID: 35698644 PMCID: PMC9188405 DOI: 10.2147/jhc.s365302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Shuhua Zhang
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Mi Jiang
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Huan Cao
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Jun Xiong
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, People’s Republic of China
| | - Jianqun Xu
- Department of Respiratory Medicine, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, 430060, People’s Republic of China
- Correspondence: Jianqun Xu, Department of Respiratory Medicine, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, 430060, People’s Republic of China, Email
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22
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Dai YZ, Liu YD, Li J, Chen MT, Huang M, Wang F, Yang QS, Yuan JH, Sun SH. METTL16 promotes hepatocellular carcinoma progression through downregulating RAB11B-AS1 in an m 6A-dependent manner. Cell Mol Biol Lett 2022; 27:41. [PMID: 35596159 PMCID: PMC9123709 DOI: 10.1186/s11658-022-00342-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/04/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The molecular mechanisms driving hepatocellular carcinoma (HCC) remain largely unclear. As one of the major epitranscriptomic modifications, N6-methyladenosine (m6A) plays key roles in HCC. The aim of this study was to investigate the expression, roles, and mechanisms of action of the RNA methyltransferase methyltransferase-like protein 16 (METTL16) in HCC. METHODS The expression of METTL16 and RAB11B-AS1 was determined by RT-qPCR. The regulation of RAB11B-AS1 by METTL16 was investigated by RNA immunoprecipitation (RIP), methylated RIP (MeRIP), and RNA stability assays. In vitro and in vivo gain- and loss-of-function assays were performed to investigate the roles of METTL16 and RAB11B-AS1. RESULTS METTL16 was upregulated in HCC, and its increased expression was correlated with poor prognosis of HCC patients. METTL16 promoted HCC cellular proliferation, migration, and invasion, repressed HCC cellular apoptosis, and promoted HCC tumoral growth in vivo. METTL16 directly bound long noncoding RNA (lncRNA) RAB11B-AS1, induced m6A modification of RAB11B-AS1, and decreased the stability of RAB11B-AS1 transcript, leading to the downregulation of RAB11B-AS1. Conversely to METTL16, RAB11B-AS1 is downregulated in HCC, and its decreased expression was correlated with poor prognosis of patients with HCC. Furthermore, the expression of RAB11B-AS1 was negatively correlated with METTL16 in HCC tissues. RAB11B-AS1 repressed HCC cellular proliferation, migration, and invasion, promoted HCC cellular apoptosis, and inhibited HCC tumoral growth in vivo. Functional rescue assays revealed that overexpression of RAB11B-AS1 reversed the oncogenic roles of METTL16 in HCC. CONCLUSIONS This study identified the METTL16/RAB11B-AS1 regulatory axis in HCC, which represented novel targets for HCC prognosis and treatment.
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Affiliation(s)
- Yun-Zhang Dai
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Yong-da Liu
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Jie Li
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Mei-Ting Chen
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Mei Huang
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Fang Wang
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China
| | - Qing-Song Yang
- Department of Interventional Radiology, Changhai Hospital, Naval Medical University, Shanghai, 20043, China.
| | - Ji-Hang Yuan
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China.
| | - Shu-Han Sun
- Department of Medical Genetics, Naval Medical University, Shanghai, 200433, China.
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Wang B, Yang S, Jia Y, Yang J, Du K, Luo Y, Li Y, Wang Z, Liu Y, Zhu B, Rai SN. PCAT19 Regulates the Proliferation and Apoptosis of Lung Cancer Cells by Inhibiting miR-25-3p via Targeting the MAP2K4 Signal Axis. Disease Markers 2022; 2022:1-18. [PMID: 35615401 PMCID: PMC9126706 DOI: 10.1155/2022/2442094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/03/2022] [Accepted: 03/17/2022] [Indexed: 11/18/2022]
Abstract
Both PCAT19 and miR-25-3p have been reported in lung cancer studies, but whether there is a correlation between the two and whether they jointly regulate the progress of lung cancer have not been reported yet. Therefore, this study carried out a further in-depth research. The expression of PCAT19 was detected in lung cancer (LC) tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR). The effect of PCAT19 on tumor growth was detected in a tumor-bearing model of nude mice. PCAT19-transfected cells were treated with Honokiol and anisomycin. The effects of PCAT19 on proliferation, apoptosis, and cycle of LC cells were investigated by biomolecule experiments. The effects of PCAT19 on the expressions of mitogen-activated protein kinase- (MAPK-) related proteins were evaluated by western blotting. The expression of PCAT19 was decreased in LC tissues and related to patient survival, tumor size, and pathology. In addition, upregulation of PCAT19 hindered LC cell proliferation, miR-25-3p expression, and the activation of extracellular regulated protein kinases (ERK) 1/2, p38, and c-Jun N-terminal kinase (JNK), while facilitating LC cell apoptosis. Furthermore, upregulation of PCAT19 reversed the effects of Honokiol and anisomycin on promoting cell proliferation and inhibiting cell apoptosis. Collectively, our findings show that upregulated PCAT19 suppresses proliferation yet promotes the apoptosis of LC cells through modulating the miR-25-3p/MAP2K4 signaling axis.
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24
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Xie J, Tian W, Tang Y, Zou Y, Zheng S, Wu L, Zeng Y, Wu S, Xie X, Xie X. Establishment of a Cell Necroptosis Index to Predict Prognosis and Drug Sensitivity for Patients With Triple-Negative Breast Cancer. Front Mol Biosci 2022; 9:834593. [PMID: 35601830 PMCID: PMC9117653 DOI: 10.3389/fmolb.2022.834593] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/04/2022] [Indexed: 12/25/2022] Open
Abstract
Background: Necroptosis has been an alternatively identified mechanism of programmed cancer cell death, which plays a significant role in cancer. However, research about necroptosis-related long noncoding RNAs (lncRNAs) in cancer are still few. Moreover, the potentially prognostic value of necroptosis-related lncRNAs and their correlation with the immune microenvironment remains unclear. The present study aimed to explore the potential prognostic value of necroptosis-related lncRNAs and their relationship to immune microenvironment in triple-negative breast cancer (TNBC). Methods: The RNA expression matrix of patients with TNBC was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Finally, 107 patients of GSE58812, 159 patients of TCGA, and 143 patients of GSE96058 were included. Necroptosis-related lncRNAs were screened by Cox regression and Pearson correlation analysis with necroptosis-related genes. By LASSO regression analysis, nine necroptosis-related lncRNAs were employed, and a cell necroptosis index (CNI) was established; then, we evaluated its prognostic value, clinical significance, pathways, immune infiltration, and chemotherapeutics efficacy. Results: Based on the CNI value, the TNBC patients were divided into high- and low-CNI groups, and the patients with high CNI had worse prognosis, more lymph node metastasis, and larger tumor (p < 0.05). The receiver operating characteristic (ROC) analysis showed that the signature performed well. The result of the infiltration proportion of different immune cell infiltration further explained that TNBC patients with high CNI had low immunogenicity, leading to poor therapeutic outcomes. Moreover, we found significant differences of the IC50 values of various chemotherapeutic drugs in the two CNI groups, which might provide a reference to make a personalized chemotherapy for them. Conclusion: The novel prognostic marker CNI could not only precisely predict the survival probability of patients with TNBC but also demonstrate a potential role in antitumor immunity and drug sensitivity.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xinhua Xie
- *Correspondence: Xinhua Xie, ; Xiaoming Xie,
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25
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Wang Z, Zhang J, Feng T, Zhang D, Pan Y, Liu X, Xu J, Qiao X, Cui W, Dong L. Construction of lncRNA-Mediated Competing Endogenous RNA Networks Correlated With T2 Asthma. Front Genet 2022; 13:872499. [PMID: 35480331 PMCID: PMC9035528 DOI: 10.3389/fgene.2022.872499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Precise classification has been reported as a central challenge in the clinical research on diagnosis and prediction of treatment efficacy in asthma. In this study, the aim was to investigate the underlying competing endogenous RNA network mechanism of asthma, especially T2 asthma, as well as to find more diagnostic biomarkers and effective therapeutic targets. Methods: Multiple sets of T2 asthma airway biopsy transcription profiles were collected, which involved long non-coding RNA (lncRNA), mRNA, and microRNA (miRNA). DIANA-LncBase, targetscan, mirwalk, and miRDB databases were employed to predict interactions between lncRNAs, miRNAs and target mRNAs. To identify mRNAs correlated with T2 asthma, differential expression and network analyses were conducted through weighted gene co-expression network analysis (WGCNA). Subsequently, the expressions of potential biomarkers were examined through qRT-PCR analysis in the T2 asthma coreinteracting cellular factor (IL-13/IL-33) induced experimental model. Lastly, the ceRNA network was confirmed by plasmid transfection and RNAi experiments in a 16HBE cell line. Results: 30 lncRNAs, 22 miRNAs and 202 mRNAs were differentially expressed in airway biopsies from T2 asthma patients. As indicated by the ROC analysis, the lncRNA, PCAT19, had high diagnostic accuracy (AUC >0.9) in distinguishing T2 asthma patients from non-T2 asthma patients and healthy controls. Furthermore, a competing ceRNA network was established, consisting of 13 lncRNAs, 12 miRNAs, as well as eight mRNAs. The reliability of this network was verified by testing several representative interactions in the network. Conclusion: To the best of our knowledge, this study has been the first to establish an lncRNA-mediated ceRNA regulatory network for studying T2 asthma. The findings of this study may elucidate the pathogenesis and help find potential therapeutic targets for T2 asthma. In T2 asthma, PCAT19-dominated ceRNA regulation networks may play a critical role, and PCAT19 may serve as a potential immune-related biomarker for asthma and other respiratory diseases correlated with eosinophilic inflammation.
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Affiliation(s)
- Zihan Wang
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jintao Zhang
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Feng
- Department of Respiratory Medicine, Shengli Oilfield Central Hospital, Dongying, China
| | - Dong Zhang
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yun Pan
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaofei Liu
- Department of Respiratory, Shandong Provincial Qianfoshan Hospital, Shandong University, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
| | - Jiawei Xu
- Department of Respiratory, Shandong Provincial Qianfoshan Hospital, Shandong University, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
| | - Xinrui Qiao
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenjing Cui
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Liang Dong
- Department of Respiratory, Shandong Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Respiratory, Shandong Provincial Qianfoshan Hospital, Shandong University, The First Affiliated Hospital of Shandong First Medical University, Shandong Institute of Respiratory Diseases, Jinan, China
- *Correspondence: Liang Dong,
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26
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Yang L, Guo G, Yu X, Wen Y, Lin Y, Zhang R, Zhao D, Huang Z, Wang G, Yan Y, Zhang X, Chen D, Xing W, Wang W, Zeng W, Zhang L. Mutation-Derived Long Noncoding RNA Signature Predicts Survival in Lung Adenocarcinoma. Front Oncol 2022; 12:780631. [PMID: 35372012 PMCID: PMC8965709 DOI: 10.3389/fonc.2022.780631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genomic instability is one of the representative features of cancer evolution. Recent research has revealed that long noncoding RNAs (lncRNAs) play a critical role in maintaining genomic instability. Our work proposed a gene signature (GILncSig) based on genomic instability-derived lncRNAs to probe the possibility of lncRNA signatures as an index of genomic instability, providing a potential new approach to identify genomic instability-related cancer biomarkers. Methods Lung adenocarcinoma (LUAD) gene expression data from an RNA-seq FPKM dataset, somatic mutation information and relevant clinical materials were downloaded from The Cancer Genome Atlas (TCGA). A prognostic model consisting of genomic instability-related lncRNAs was constructed, termed GILncSig, to calculate the risk score. We validated GILncSig using data from the Gene Expression Omnibus (GEO) database. In this study, we used R software for data analysis. Results Through univariate and multivariate Cox regression analyses, five genomic instability-associated lncRNAs (LINC01671, LINC01116, LINC01214, lncRNA PTCSC3, and LINC02555) were identified. We constructed a lncRNA signature (GILncSig) related to genomic instability. LUAD patients were classified into two risk groups by GILncSig. The results showed that the survival rate of LUAD patients in the low-risk group was higher than that of those in the high-risk group. Then, we verified GILncSig in the GEO database. GILncSig was associated with the genomic mutation rate of LUAD. We also used GILncSig to divide TP53 mutant-type patients and TP53 wild-type patients into two groups and performed prognostic analysis. The results suggested that compared with TP53 mutation status, GILncSig may have better prognostic significance. Conclusions By combining the lncRNA expression profiles associated with somatic mutations and the corresponding clinical characteristics of LUAD, a lncRNA signature (GILncSig) related to genomic instability was established.
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Affiliation(s)
- Longjun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongbin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongtai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Xing
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weidong Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weian Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Xu Y, Lin G, Liu Y, Lin X, Lin H, Guo Z, Xu Y, Lin Q, Chen S, Yang J, Zeng Y. An integrated analysis of the competing endogenous RNA network associated of prognosis of stage I lung adenocarcinoma. BMC Cancer 2022; 22:188. [PMID: 35183135 PMCID: PMC8857797 DOI: 10.1186/s12885-022-09290-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/08/2022] [Indexed: 12/25/2022] Open
Abstract
Abstract
Background
Accumulating evidence indicates that long non-coding RNAs (lncRNAs) are involving in the tumorigenesis and metastasis of lung cancer. The aim of the study is to systematically characterize the lncRNA-associated competing endogenous RNA (ceRNA) network and identify key lncRNAs in the development of stage I lung adenocarcinoma (LUAD).
Methods
Totally, 1,955 DEmRNAs, 165 DEmiRNAs and 1,107 DElncRNAs were obtained in 10 paired normal and LUAD tissues. And a total of 8,912 paired lncRNA-miRNA-mRNA network was constructed. Using the Cancer Genome Atlas (TCGA) dataset, the module of ME turquoise was revealed to be most relevant to the progression of LUAD though Weighted Gene Co-expression Network Analysis (WGCNA).
Results
Of the lncRNAs identified, LINC00639, RP4-676L2.1 and FENDRR were in ceRNA network established by our RNA-sequencing dataset. Using univariate Cox regression analysis, FENDRR was a risk factor of progression free survival (PFS) of stage I LUAD patients (HRs = 1.69, 95%CI 1.07–2.68, P < .050). Subsequently, diffe rential expression of FENDRR in paired normal and LUAD tissues was detected significant by real-time quantitative (qRT-PCR) (P < 0.001).
Conclusions
This study, for the first time, deciphered the regulatory role of FENDRR/miR-6815-5p axis in the progression of early-stage LUAD, which is needed to be established in vitro and in vivo.
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Wei H, Xu Z, Chen L, Wei Q, Huang Z, Liu G, Li W, Wang J, Tang Q, Pu J. Long non-coding RNA PAARH promotes hepatocellular carcinoma progression and angiogenesis via upregulating HOTTIP and activating HIF-1α/VEGF signaling. Cell Death Dis 2022; 13:102. [PMID: 35110549 DOI: 10.1038/s41419-022-04505-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading lethal malignancies and a hypervascular tumor. Although some long non-coding RNAs (lncRNAs) have been revealed to be involved in HCC. The contributions of lncRNAs to HCC progression and angiogenesis are still largely unknown. In this study, we identified a HCC-related lncRNA, CMB9-22P13.1, which was highly expressed and correlated with advanced stage, vascular invasion, and poor survival in HCC. We named this lncRNA Progression and Angiogenesis Associated RNA in HCC (PAARH). Gain- and loss-of function assays revealed that PAARH facilitated HCC cellular growth, migration, and invasion, repressed HCC cellular apoptosis, and promoted HCC tumor growth and angiogenesis in vivo. PAARH functioned as a competing endogenous RNA to upregulate HOTTIP via sponging miR-6760-5p, miR-6512-3p, miR-1298-5p, miR-6720-5p, miR-4516, and miR-6782-5p. The expression of PAARH was significantly positively associated with HOTTIP in HCC tissues. Functional rescue assays verified that HOTTIP was a critical mediator of the roles of PAARH in modulating HCC cellular growth, apoptosis, migration, and invasion. Furthermore, PAARH was found to physically bind hypoxia inducible factor-1 subunit alpha (HIF-1α), facilitate the recruitment of HIF-1α to VEGF promoter, and activate VEGF expression under hypoxia, which was responsible for the roles of PAARH in promoting angiogenesis. The expression of PAARH was positively associated with VEGF expression and microvessel density in HCC tissues. In conclusion, these findings demonstrated that PAARH promoted HCC progression and angiogenesis via upregulating HOTTIP and activating HIF-1α/VEGF signaling. PAARH represents a potential prognostic biomarker and therapeutic target for HCC.
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Hu Z, Zhu L, Zhang Y, Chen B. N6-methyladenosine-induced SVIL antisense RNA 1 restrains lung adenocarcinoma cell proliferation by destabilizing E2F1. Bioengineered 2022; 13:3093-3107. [PMID: 35068325 PMCID: PMC8973833 DOI: 10.1080/21655979.2022.2025697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence indicates that N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play crucial roles in cancer development. However, the biological roles of m6A and lncRNAs in lung cancer tumorigenesis are largely unknown. In this study, SVIL antisense RNA 1 (SVIL-AS1) was downregulated in lung adenocarcinoma (LUAD) tissues and was associated with a favorable prognosis in patients with LUAD. SVIL-AS1 overexpression suppressed LUAD cell proliferation and blocked cell cycle arrest. Mechanistically, METTL3 increased the m6A modification and transcript stability of SVIL-AS1. The enhanced SVIL-AS1 expression mediated by METTL3 suppressed E2F1 and E2F1-target genes. Moreover, SVIL-AS1 accelerated E2F1 degradation. The reduction in cell proliferation induced by SVIL-AS1 overexpression could be rescued by E2F1 overexpression or METTL3 knockdown. In conclusion, our work demonstrated the role and mechanism of METTL3-induced SVIL-AS1 in LUAD, which connects m6A and lncRNA in lung cancer carcinogenesis.
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Affiliation(s)
- Zedong Hu
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Liang Zhu
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Yilin Zhang
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Bing Chen
- Second Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
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Zhang S, Xu J, Cao H, Jiang M, Xiong J. KB-68A7.1 Inhibits Hepatocellular Carcinoma Development Through Binding to NSD1 and Suppressing Wnt/β-Catenin Signalling. Front Oncol 2022; 11:808291. [PMID: 35127520 PMCID: PMC8810504 DOI: 10.3389/fonc.2021.808291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with extremely poor prognosis. Therefore, revealing the critical molecules involved in HCC progression and prognosis is urgently needed. In this study, through combining public dataset and our cohort, we found a novel prognosis-related long non-coding RNA KB-68A7.1 in HCC. KB-68A7.1 was lowly expressed in HCC, whose low expression was associated with large tumour size, aggressive clinical characteristic, and poor survival. Gain- and loss-of-function assays demonstrated that KB-68A7.1 restricted HCC cellular proliferation, induced HCC cellular apoptosis, and suppressed HCC cellular migration and invasion in vitro. Xenograft assays demonstrated that KB-68A7.1 suppressed HCC tumour growth and metastasis in vivo. These functional assays suggested KB-68A7.1 as a tumour suppressor in HCC. Histone methyltransferase nuclear receptor binding SET domain-containing protein 1 (NSD1) was found to bind to KB-68A7.1. KB-68A7.1 was mainly distributed in the cytoplasm. The binding of KB-68A7.1 to NSD1 sequestrated NSD1 in the cytoplasm, leading to the reduction in nuclear NSD1 level. Through decreasing nuclear NSD1 level, KB-68A7.1 reduced di-methylation of histone H3 at lysine 36 (H3K36me2) and increased tri-methylation of histone H3 at lysine 27 (H3K27me3) at the promoter of WNT10B, a target of NSD1. Thus, KB-68A7.1 repressed WNT10B transcription. The expression of WNT10B was negatively correlated with that of KB-68A7.1 in HCC tissues. Through repressing WNT10B, KB-68A7.1 further repressed Wnt/β-catenin signalling. Functional rescue assays showed that overexpression of WNT10B reversed the tumour-suppressive roles of KB-68A7.1, whereas the oncogenic roles of KB-68A7.1 depletion were abolished by Wnt/β-catenin signalling inhibitor. Overall, this study identified KB-68A7.1 as a lowly expressed and prognosis-related lncRNA in HCC, which suppressed HCC progression through binding to NSD1 and repressing Wnt/β-catenin signalling.
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Affiliation(s)
- Shuhua Zhang
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianqun Xu
- Department of Respiratory Medicine, Wuhan Third Hospital, Tongren Hospital of Wuhan University, Wuhan, China
- *Correspondence: Jianqun Xu,
| | - Huan Cao
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mi Jiang
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Xiong
- Department of Hepatobiliary Surgery of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Abstract
PURPOSE: Functions associated with glycolysis could serve as targets or biomarkers for therapy cancer. Our purpose was to establish a prognostic model that could evaluate the importance of Glycolysis-related lncRNAs in breast cancer. METHODS: Gene expressions were evaluated for breast cancer through The Cancer Genome Atlas (TCGA) database, and we calculated Pearson correlations to discover potential related lncRNAs. Differentially expressed genes were identified via criteria of FDR < 0.05 and |FC|> 2. Total samples were separated into training and validating sets randomly. Univariate Cox regression identified 14 prognostic lncRNAs in training set. A prognostic model was constructed to evaluate the accuracy in predicting prognosis. The univariate and multivariate Cox analysis were performed to verify whether lncRNA signature could be an independent prognostic factor The signature was validated in validating set. Immune infiltration levels were assessed. RESULTS: Eighty-nine differentially expressed lncRNAs were identified from 420 Glycolysis-related lncRNAs. 14 lncRNAs were correlated with prognosis in training set and were selected to establish the prognostic model. Low risk group had better prognosis in both training (p= 9.025 e -10) and validating (p= 4.272 e -3) sets. The univariate and multivariate Cox analysis revealed that risk score of glycolysis-related lncRNAs (P< 0.001) was an independent prognostic factor in both training and validating sets. The neutrophils (p= 4.214 e -13, r=-0.223), CD4+ T cells (p= 1.833 e -20, r=-0.283), CD8+ T cells (p= 7.641 e -12, r=-0.211), B cells (p= 2.502 e -10, r=-0.195) and dendritic cells (p= 5.14 e -18, r=-0.265) were negatively correlated with risk score of prognostic model. The Macrophage (p= 0.016, r= 0.0755) was positively correlated with the risk score. CONCLUSION: Our study indicated that glycolysis-related lncRNAs had a significant role to facilitate the individualized survival prediction in breast cancer patients, which would be a potential therapeutic target.
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Affiliation(s)
- Jiayue Zou
- Department of Hepatobiliary Surgery, General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yanlin Gu
- Department of Thyroid and Breast Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qi Zhu
- Department of Thyroid and Breast Surgery, Traditional Chinese Medicine Hospital of Kunshan, Kunshan, Jiangsu, China
| | - Xiaohua Li
- Department of Thyroid and Breast Surgery, Wuzhong People’s Hospital of Suzhou City, Suzhou, Jiangsu, China
| | - Lei Qin
- Department of Hepatobiliary Surgery, General Surgery, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Lamas NJ, Martel A, Nahon-Estève S, Goffinet S, Macocco A, Bertolotto C, Lassalle S, Hofman P. Prognostic Biomarkers in Uveal Melanoma: The Status Quo, Recent Advances and Future Directions. Cancers (Basel) 2021; 14:96. [PMID: 35008260 DOI: 10.3390/cancers14010096] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Although rare, uveal melanoma (UM) is the most common cancer that develops inside adult eyes. The prognosis is poor, since 50% of patients will develop lethal metastases in the first decade, especially to the liver. Once metastases are detected, life expectancy is limited, given that the available treatments are mostly unsuccessful. Thus, there is a need to find methods that can accurately predict UM prognosis and also effective therapeutic strategies to treat this cancer. In this manuscript, we initially compile the current knowledge on epidemiological, clinical, pathological and molecular features of UM. Then, we cover the most relevant prognostic factors currently used for the evaluation and follow-up of UM patients. Afterwards, we highlight emerging molecular markers in UM published over the last three years. Finally, we discuss the problems preventing meaningful advances in the treatment and prognostication of UM patients, as well as forecast new roadblocks and paths of UM-related research. Abstract Uveal melanoma (UM) is the most common malignant intraocular tumour in the adult population. It is a rare cancer with an incidence of nearly five cases per million inhabitants per year, which develops from the uncontrolled proliferation of melanocytes in the choroid (≈90%), ciliary body (≈6%) or iris (≈4%). Patients initially present either with symptoms like blurred vision or photopsia, or without symptoms, with the tumour being detected in routine eye exams. Over the course of the disease, metastases, which are initially dormant, develop in nearly 50% of patients, preferentially in the liver. Despite decades of intensive research, the only approach proven to mildly control disease spread are early treatments directed to ablate liver metastases, such as surgical excision or chemoembolization. However, most patients have a limited life expectancy once metastases are detected, since there are limited therapeutic approaches for the metastatic disease, including immunotherapy, which unlike in cutaneous melanoma, has been mostly ineffective for UM patients. Therefore, in order to offer the best care possible to these patients, there is an urgent need to find robust models that can accurately predict the prognosis of UM, as well as therapeutic strategies that effectively block and/or limit the spread of the metastatic disease. Here, we initially summarized the current knowledge about UM by compiling the most relevant epidemiological, clinical, pathological and molecular data. Then, we revisited the most important prognostic factors currently used for the evaluation and follow-up of primary UM cases. Afterwards, we addressed emerging prognostic biomarkers in UM, by comprehensively reviewing gene signatures, immunohistochemistry-based markers and proteomic markers resulting from research studies conducted over the past three years. Finally, we discussed the current hurdles in the field and anticipated the future challenges and novel avenues of research in UM.
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Wang Z, Liu Y, Zhang J, Zhao R, Zhou X, Wang H. An Immune-Related Long Noncoding RNA Signature as a Prognostic Biomarker for Human Endometrial Cancer. J Oncol 2021; 2021:9972454. [PMID: 34925511 DOI: 10.1155/2021/9972454] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022]
Abstract
Background Endometrial cancer is among the most common malignant tumors threatening the health of women. Recently, immunity and long noncoding RNA (lncRNA) have been widely examined in oncology and shown to play important roles in oncology. Here, we searched for immune-related lncRNAs as prognostic biomarkers to predict the outcome of patients with endometrial cancer. Methods RNA sequencing data for 575 endometrial cancer samples and immune-related genes were downloaded from The Cancer Genome Atlas (TCGA) database and gene set enrichment analysis (GSEA) gene sets, respectively. Immune-related lncRNAs showing a coexpression relationship with immune-related genes were obtained, and Cox regression analysis was performed to construct the prognostic model. Survival, independent prognostic, and clinical correlation analyses were performed to evaluate the prognostic model. Immune infiltration of endometrial cancer samples was also evaluated. Functional annotation of 12 immune-related lncRNAs was performed using GSEA software. Prognostic nomogram and survival analysis for independent prognostic risk factors were performed to evaluate the prognostic model and calculate the survival time based on the prognostic model. Results Twelve immune-related lncRNAs (ELN-AS1, AC103563.7, PCAT19, AF131215.5, LINC01871, AC084117.1, NRAV, SCARNA9, AL049539.1, POC1B-AS1, AC108134.4, and AC019080.5) were obtained, and a prognostic model was constructed. The survival rate in the high-risk group was significantly lower than that in the low-risk group. Patient age, pathological grade, the International Federation of Gynecology and Obstetrics (FIGO) stage, and risk status were the risk factors. The 12 immune-related lncRNAs correlated with patient age, pathological grade, and FIGO stage. Principal component analysis and functional annotation showed that the high-risk and low-risk groups separated better, and the immune status of the high-risk and low-risk groups differed. Nomogram and receiver operating characteristic (ROC) curves effectively predicted the prognosis of endometrial cancer. Additionally, age, pathological grade, FIGO stage, and risk status were all related to patient survival. Conclusion We identified 12 immune-related lncRNAs affecting the prognosis of endometrial cancer, which may be useful as therapeutic targets and molecular biomarkers.
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Jiang F, Lv Q, Hu C, Li Z, Wu H, Gao S, Wang H, Zhao Y, Shao Q. PCAT6 May Be a Whistler and Checkpoint Target for Precision Therapy in Human Cancers. Cancers (Basel) 2021; 13:6101. [PMID: 34885209 DOI: 10.3390/cancers13236101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Prostate cancer-associated transcript 6 (PCAT6), as a newly discovered carcinogenic long non-coding RNA (lncRNA), is abnormally expressed in multiple diseases. With the accumulation of studies on PCAT6, we have a deeper understanding of its biological functions and mechanisms. Therefore, in this review, the various molecular mechanisms by which PCAT6 promotes multiple tumorigenesis and progression are summarized and discussed. Furthermore, its potential diagnostic, prognostic, and immunotherapeutic values are also clarified. Abstract LncRNAs are involved in the occurrence and progressions of multiple cancers. Emerging evidence has shown that PCAT6, a newly discovered carcinogenic lncRNA, is abnormally elevated in various human malignant tumors. Until now, PCAT6 has been found to sponge various miRNAs to activate the signaling pathways, which further affects tumor cell proliferation, migration, invasion, cycle, apoptosis, radioresistance, and chemoresistance. Moreover, PCAT6 has been shown to exert biological functions beyond ceRNAs. In this review, we summarize the biological characteristics of PCAT6 in a variety of human malignancies and describe the biological mechanisms by which PCAT6 can facilitate tumor progression. Finally, we discuss its diagnostic and prognostic values and clinical applications in various human malignancies.
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Lin Z, Huang W, Yi Y, Li D, Xie Z, Li Z, Ye M. LncRNA ADAMTS9-AS2 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Lung Adenocarcinoma. Int J Gen Med 2021; 14:8541-8555. [PMID: 34849000 PMCID: PMC8626860 DOI: 10.2147/ijgm.s340683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022] Open
Abstract
Background The role of long noncoding RNA (LncRNA) ADAMTS9 antisense RNA 2 (ADAMTS9-AS2) is unclear in lung adenocarcinoma (LUAD). The aim of this study was to explore the relationship between ADAMTS9-AS2 and LUAD, based on The Cancer Genome Atlas (TCGA) database and bioinformatics analysis. Methods Various statistical methods, Kaplan–Meier method, Cox regression analysis, GSEA, and immune infiltration analysis were used to evaluate the relationship between clinical features and ADAMTS9-AS2 expression, prognostic factors, and the significant involvement of ADAMTS9-AS2 in function. Results In LUAD patients, low expression of ADAMTS9-AS2 was associated with N stage (P=0.011), gender (P=0.002), number of packs smoked (P=0.024) and smoker (P<0.001). Low ADAMTS9-AS2 expression predicted a poorer overall survival (OS) (HR: 0.68; 95% CI: 0.51–0.91; P=0.01). And ADAMTS9-AS2 expression (HR: 0.626; 95% CI: 0.397–0.986; P=0.043) was independently correlated with OS in LUAD patients. Unwinding of DNA, extrinsic pathway, polo-like kinase-mediated events, cori cycle, MCM pathway, proteasome pathway, lagging strand synthesis and PCNA-dependent long patch base excision repair were differentially enriched in ADAMTS9-AS2 high expression phenotype. ADAMTS9-AS2 expression was correlated with certain immune infiltrating cells. Conclusion In LUAD patients, ADAMTS9-AS2 expression was significantly associated with poor survival and immune infiltration. ADAMTS9-AS2 may be a promising biomarker of prognosis and response to immunotherapy for LUAD.
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Affiliation(s)
- Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Yongsheng Yi
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Dongbing Li
- MyGene Diagnostics Co., Ltd., Guangzhou, 510000, Guangdong, People's Republic of China
| | - Zehua Xie
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Zumei Li
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
| | - Min Ye
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, Guangdong, People's Republic of China
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Li N, Zhang H, Hu K, Chu J. A novel long non-coding RNA-based prognostic signature for renal cell carcinoma patients with stage IV and histological grade G4. Bioengineered 2021; 12:6275-6285. [PMID: 34499010 PMCID: PMC8806408 DOI: 10.1080/21655979.2021.1971022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/02/2022] Open
Abstract
This study aimed to establish a lncRNA-based signature for predicting the prognosis of patients with high stage and grade renal cell carcinoma (RCC). According to the Surveillance, Epidemiology, and End Results (SEER) database, sex, age, grade, stage, surgery, chemotherapy, radiation, tumor size, and marital status were the independent prognostic factors for RCC and also had significant correlations with the overall survival through Cox univariate and multivariate analyses. Noticeably, among these influencing factors, the histological classification of undifferentiated group and pathological stage IV had the greatest prognostic risks for RCC patients. Furthermore, based on the samples at stage IV and histological grade G4 from The Cancer Genome Atlas (TCGA) portal, 9 key lncRNAs, including KIAA2012, CCNT2-AS1, ITPKB-AS1, TBX2-AS1, NUTM2A-AS1, LINC02522, LINC02384, LINC01559, and LINC00865 were identified and a prognostic signature was constructed by Lasso analysis and Cox regression model. The Kaplan-Meier analysis suggested that patients at stage IV and histological grade of G4 in high risk score group had a worse overall survival than that in low risk score group. The following receiver operating characteristic curve (ROC) curves also showed that this signature possesses a better predictive power performance. Pathway enrichment analysis discovered that 9 lncRNAs held potential roles in cell division, cell cycle, DNA damage and cytokines levels in RCC. This work indicates that the established 9-lncRNA signature has a good capacity in predicting the prognosis of RCC patients with stage IV and histological grade of G4, and may be helpful for guiding the treatment strategies for RCC patients.
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Affiliation(s)
- Ning Li
- Department of Urology, Yantaishan Hospital, Yantai, Shandong , P.R. China
| | - Haiying Zhang
- Department of Urology, Yantaishan Hospital, Yantai, Shandong , P.R. China
| | - Keyao Hu
- Department of Urology, Yantaishan Hospital, Yantai, Shandong , P.R. China
| | - Jianfeng Chu
- Department of Urology, Yantaishan Hospital, Yantai, Shandong , P.R. China
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Pu J, Zhang Y, Wang A, Qin Z, Zhuo C, Li W, Xu Z, Tang Q, Wang J, Wei H. ADORA2A-AS1 Restricts Hepatocellular Carcinoma Progression via Binding HuR and Repressing FSCN1/AKT Axis. Front Oncol 2021; 11:754835. [PMID: 34733789 PMCID: PMC8558402 DOI: 10.3389/fonc.2021.754835] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most aggressive malignancies. Increasing evidence revealed that long noncoding RNAs (lncRNAs) were frequently involved in various malignancies. Here, we explored the clinical significances, roles, and mechanisms of lncRNA ADORA2A antisense RNA 1 (ADORA2A-AS1) in HCC. Methods The clinical significances of ADORA2A-AS1 in HCC were analyzed using RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) project. The expressions of ADORA2A-AS1, Fascin Actin-Bundling Protein 1 (FSCN1), Matrix Metallopeptidase 2 (MMP2), and Baculoviral IAP Repeat Containing 7 (BIRC7) in HCC tissues and cells were measured by qRT-PCR. Cell Counting Kit-8 (CCK-8), 5-ethynyl-2’-deoxyuridine (EdU), caspase-3 activity assay, transwell migration and invasion assays, and xenograft growth and metastasis experiments were performed to evaluate the roles of ADORA2A-AS1 in HCC. RNA pull-down, RNA immunoprecipitation, qRT-PCR, Western blot, and RNA stability assay were performed to elucidate the mechanisms of ADORA2A-AS1 in HCC. Results ADORA2A-AS1 was identified as an HCC-related lncRNA, whose low expression was correlated with advanced stage and poor outcome in HCC. Gain- and loss-of functional experiments demonstrated that ADORA2A-AS1 inhibited HCC cell proliferation, induced cell apoptosis, repressed cell migration and invasion, and repressed xenograft growth and metastasis in vivo. Mechanistically, ADORA2A-AS1 competitively bound HuR (Hu Antigen R), repressed the binding of HuR to FSCN1 transcript, decreased FSCN1 transcript stability, and downregulated FSCN1 expression. The expression of FSCN1 was negatively correlated with ADORA2A-AS1 in HCC tissues. Through downregulating FSCN1, ADORA2A-AS1 repressed AKT pathway activation. Functional rescue assays showed that blocking of FSCN1/AKT axis abrogated the roles of ADORA2A-AS1 in HCC. Conclusion Low-expression ADORA2A-AS1 is correlated with poor survival of HCC patients. ADORA2A-AS1 exerts tumor-suppressive roles in HCC via binding HuR and repressing FSCN1/AKT axis.
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Affiliation(s)
- Jian Pu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Ya Zhang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Anmin Wang
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Zebang Qin
- Graduate College of Youjiang Medical University for Nationalities, Baise, China
| | - Chenyi Zhuo
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenchuan Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zuoming Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qianli Tang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Jianchu Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Huamei Wei
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Wang J, Zha J, Wang X. Knockdown of lncRNA NUTM2A-AS1 inhibits lung adenocarcinoma cell viability by regulating the miR-590-5p/METTL3 axis. Oncol Lett 2021; 22:798. [PMID: 34630705 PMCID: PMC8477074 DOI: 10.3892/ol.2021.13059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer-related mortality worldwide. Long non-coding RNA (lncRNA) NUT family member 2A antisense RNA 1 (NUTM2A-AS1) is dysregulated in LUAD; however, its role in this disease remains unclear. The present study aimed to identify the underlying molecular mechanism of the effect of lncRNA NUTM2A-AS1 in LUAD by exploring whether lncRNA NUTM2A-AS1 could affect LUAD cell proliferation and apoptosis through the microRNA (miR)-590-5p/methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3) axis. miR-590-5p was predicted and verified as the direct target of NUTM2A-AS1 using bioinformatics analysis and a dual luciferase reporter assay. The expression levels of NUTM2A-AS1 and miR-590-5p in lung cancer cells, and the effects of NUTM2A-AS1 on cell viability and apoptosis were determined using MTT assays and flow cytometry, respectively. Reverse transcription-quantitative PCR analysis revealed that the expression levels of NUTM2A-AS1 were significantly upregulated, while those of miR-590-5p were significantly downregulated, in lung cancer cells compared with the control epithelial cells. NUTM2A-AS1 knockdown inhibited NCI-H23 cell viability and induced apoptosis by upregulating miR-590-5p expression. Moreover, the function and regulatory mechanism of miR-590-5p in LUAD were also investigated. It was determined that miR-590-5p could interact with METTL3, and further analysis of the expression levels of METTL3 in lung cancer cells demonstrated that METTL3 was significantly upregulated in NCI-H23 and A549 cells compared with the control cells. In addition, miR-590-5p inhibited NCI-H23 cell viability and induced apoptosis by downregulating METTL3 expression. In conclusion, the findings of the present study suggested that NUTM2A-AS1 knockdown may inhibit LUAD progression by regulating the miR-590-5p/METTL3 axis. These results may provide insight into the mechanisms underlying the tumorigenesis of LUAD and offer a new treatment strategy for the disease.
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Affiliation(s)
- Jie Wang
- Department of Thoracic Surgery, Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Jingyun Zha
- Department of Respiratory Medicine, Hefei First People's Hospital, Hefei, Anhui 230001, P.R. China
| | - Xiaolin Wang
- Department of Thoracic Surgery, Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
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Wu C, Bian X, Zhang L, Hu Y, Wu Y, Pei T, Han X. Long noncoding RNA LINC00968 inhibits proliferation, migration and invasion of lung adenocarcinoma through targeting miR-22-5p/CDC14A axis. 3 Biotech 2021; 11:433. [PMID: 34603911 PMCID: PMC8440738 DOI: 10.1007/s13205-021-02981-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a high aggressive human cancer which usually diagnosed at advanced stages. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) are crucial participants in LUAD progression. In the present study, we found that lncRNA LINC00968 was significantly down-regulated in LUAD tissues and cell lines. LINC00968 level was positively correlated to survival rate, and negatively correlated to tumor node metastasis (TNM) stage, tumor size and lymph node metastasis of LUAD patients. We over-expressed LINC00968 in LUAD cells using lentivirus, inhibited proliferation and cell cycle arrest at G1 phase were detected. LINC00968 over-expression also suppressed migration, invasion and epithelial mesenchymal transition. We further validated that LINC00968 localized in cytoplasm and acted as an upstream regulator of microRNA miR-22-5p, which was up-regulated in LUAD tissues and cell lines. Besides, elevated miR-22-5p expression abolished the effect of LINC00968 over-expression on LUAD progression including in vivo tumor growth. In addition, we first validated that cell division cycle 14A (CDC14A), which was down-regulated in LUAD tissues, was a downstream target of miR-22-5p. We over-expressed CDC14A in LUAD cells and miR-22-5p induced LUAD progression was partially reversed. In conclusion, our study demonstrated that LINC00968 inhibited proliferation, migration and invasion of LUAD by sponging miR-22-5p and further restoring CDC14A. This novel regulatory axis might provide us with promising diagnostic and therapeutic target in LUAD treatment.
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Affiliation(s)
- Chao Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Xuzhao Bian
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Liyuan Zhang
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yuanyuan Hu
- Medical College, Xijing University, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yang Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Tianli Pei
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - XinPeng Han
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Ebrahimzadeh K. A review on the role of PCAT6 lncRNA in tumorigenesis. Biomed Pharmacother 2021; 142:112010. [PMID: 34388529 DOI: 10.1016/j.biopha.2021.112010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer-associated transcript 6 (PCAT6) is a long non-coding RNA (lncRNA) firstly identified in 2013 through an integrative genomic analysis of different cancer tissues. This oncogenic lncRNA has been found to regulate carcinogenesis process in different tissues, including breast, ovary, stomach, bladder, colon, pancreas and liver. The role of PCAT6 in sequestering certain microRNAs has been well established. For instance, miR-4723-5p, miR-185-5p, miR-143-3p, miR-30, miR-15a, miR-513a and miR-204, and miR-326 are among those being sequestered by PCAT6. Over-expression of PCAT6 has been associated with poor clinical outcomes in diverse types of cancers including ovarian, bladder, colorectal and pancreatic cancers. In the present review, we summarize the impact of PCAT6 in the development of diverse types of cancers, based on the results of functional studies in cell lines, experiments in xenograft models of cancers and expression studies in samples obtained from human subjects.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Abdul-Maksoud RS, Rashad NM, Elsayed WSH, Elsayed RS, Sherif MM, Abbas A, El Shabrawy M. The diagnostic significance of circulating lncRNA ADAMTS9-AS2 tumor biomarker in non-small cell lung cancer among the Egyptian population. J Gene Med 2021; 23:e3381. [PMID: 34312940 DOI: 10.1002/jgm.3381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/29/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Long non-coding RNA ADAM metallopeptidase with thrombospondin type 1 motif, 9 antisense RNA 2 (ADAMTS9-AS2) was recognized as a novel tumor suppressor and plays an important role in the initiation and progression of malignant behavior in human cancers, although its plasma expression and clinical value in patients with non-small cell lung cancer (NSCLC) remain unknown. We aimed to analyze the diagnostic role of ADAMTS9-AS2 and cytokeratin 19 fragmentation antigen (CYFRA 21-1) in NSCLC. METHODS The present study included 80 control subjects, 80 patients with benign lung lesion and 80 NSCLC patients. The expression of ADAMTS9-AS2 in the tissue and plasma was detected by a real-time polymerase chain reaction. Serum CYFRA 21-1 was analyzed using an enzyme-linked immunosorbent assay. RESULTS In comparison with benign lung lesion and controls, tissue and plasma ADAMTS9-AS2 expression were significantly down-regulated in NSCLC (p < 0.001). Decreased ADAMTS9-AS2 expression was associated with TNM stages in NSCLC patients (p < 0.001). Up-regulation of CYFRA 21-1 was reported among NSCLC patients and it was associated with TNM staging. Tissue and plasma ADAMTS9-AS2 expression levels were the predicting factors for NSCLC and they both correlated negatively with CYFRA 21-1 levels. Plasma ADAMTS9-AS2 levels had a significant positive correlation with their tumor tissue levels. Plasma ADAMTS9-AS2 showed a higher sensitivity (95%) and specificity (99.1%) in the diagnosis of NSCLC than CYFRA 21-1 (61.3% sensitivity and 60% specificity). CONCLUSIONS Our results suggested that decreased plasma ADAMTS9-AS2 expression might act as a novel non-invasive tumor biomarker in NSCLC diagnosis. Furthermore, plasma ADAMTS9-AS2 might predict aggressive tumor behavior.
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Affiliation(s)
- Rehab S Abdul-Maksoud
- Medical Biochemistry Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Nearmeen M Rashad
- Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Walid S H Elsayed
- Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Rasha S Elsayed
- General Surgery Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Magda M Sherif
- Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmad Abbas
- Chest department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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Guo L, Ding L, Tang J. Identification of a competing endogenous RNA axis "SVIL-AS1/miR-103a/ICE1" associated with chemoresistance in lung adenocarcinoma by comprehensive bioinformatics analysis. Cancer Med 2021; 10:6022-6034. [PMID: 34264003 PMCID: PMC8419767 DOI: 10.1002/cam4.4132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/19/2022] Open
Abstract
Background Chemotherapy is an important treatment for lung cancer. The molecular mechanism of lung adenocarcinoma (LUAD) chemoresistance is not completely understood. Methods Weighted gene co‐expression network analysis (WGCNA) was applied to screen the modules related to chemosensitivity using the data of LUAD patients receiving chemotherapy in The Cancer Genome Atlas database. GDCRNATools package was used to establish competing endogenous RNA (ceRNA) network based on the key chemotherapy‐related module. Kaplan–Meier and risk models were used to analyze the influence of genes in the ceRNA network on the prognosis of LUAD patients receiving chemotherapy. Cell counting kit‐8, reverse transcription‐quantitative PCR, and dual‐luciferase reporter assay were used to detect the effects of abnormal expression of genes in the ceRNA network on the proliferation and IC50 of cisplatin (DDP)‐resistant LUAD cells, and the targeting relationship of genes in the ceRNA network. The signaling pathways and functions of ICE1 in LUAD were analyzed by LinkOmics and CancerSEA databases, and validated by Western blot. Results Midnightblue module was the only WGCNA module positively correlated with chemosensitivity, in which the function of genes was related to cancer progression. SVIL‐AS1/miR‐103a/ICE1 was constructed based on midnightblue module. High expression of SVIl‐AS1 and ICE1 corresponded to a favorable prognosis. High expression of miR‐103a corresponded to a dismal prognosis. SVIl‐AS1 was downregulated in DDP‐resistant LUAD cells. SVIL‐AS1 overexpression retarded the proliferation and DDP resistance of DDP‐resistant LUAD cell. miR‐103a was sponged by SVIL‐AS1 and directly targeted ICE1. miR‐103a overexpression and ICE1 knockdown overturned the suppressive effect of SVIL‐AS1 overexpression on cell proliferation and DDP resistance. Further bioinformatics analysis and experimental verification showed that SVIL‐AS1/miR‐103a‐3p/ICE1 axis can enhance DNA damage caused by chemotherapeutic agents. Conclusions SVIL‐AS1 inhibited chemoresistance by acting as a sponge for miR‐103a and upregulating ICE1 expression, which may be a potential therapeutic target for chemotherapy in LUAD.
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Affiliation(s)
- Lili Guo
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lina Ding
- Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Ministry of Education of China, Zhengzhou University, Zhengzhou, P.R. China
| | - Junfang Tang
- Department of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
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Abstract
Long non-coding RNA (lncRNA) PCAT6 is a member of the Prostate Cancer Associated Transcripts family of molecules. In this review, we focus on the latest studies involving PCAT6 in the diagnosis, treatment, and prognosis of malignant tumors of the digestive, respiratory, urinary, reproductive, motion, and nervous systems. PCAT6 was found to be highly expressed in gastric cancer, colon cancer, hepatocellular carcinoma, lung cancer, bladder cancer, ovarian cancer, breast cancer, cervical cancer, osteosarcoma, glioblastoma, and other tumors. PCAT6 can promote the development and progression of different types of malignant tumors through various mechanisms. Overall, these findings suggest that PCAT6 may play an increasingly vital role in the clinical assessment of these malignant tumors. It can function as an oncogene and may be used as a potential new prognostic biomarker of these tumors.
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Affiliation(s)
- Siying Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Fang C, Liu F, Wang Y, Yuan S, Chen R, Qiu X, Qian X, Zhang X, Xiao Z, Wang Q, Fu B, Li Y. A innovative prognostic symbol based on neutrophil extracellular traps (NETs)-related lncRNA signature in non-small-cell lung cancer. Aging (Albany NY) 2021; 13:17864-79. [PMID: 34257164 DOI: 10.18632/aging.203289] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Neutrophil extracellular traps (NETs) are closely related to cancer progression. NETs-related lncRNAs play crucial roles in non-small-cell lung cancer (NSCLC) but there have been no systematic studies regarding NETs-related long noncoding RNA (lncRNA) signatures to forecast the prognosis of NSCLC patients. It’s essential to build commensurate NETs-related lncRNA signatures. The expression profiles of prognostic mRNAs and lncRNAs and relevant clinical data of NSCLC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The NETs-related genes came from the results of our transcriptome RNA microarray data. The co-expression network of lncRNAs and NETs-related genes was structured to confirm NETs-related lncRNAs. The 19 lncRNAs correlated with overall survival (OS) were selected by exploiting univariate Cox regression (P < 0.05). Lasso regression and multivariate Cox regression (P < 0.05) were utilized to develop a 12-NETs-related lncRNA signature. We established a risk score based on the signature, which suggested that patients in the high-risk group displayed significantly shorter OS than patients in the low-risk group (P < 0.0001, P = 0.0023 respectively in the two cohorts). The risk score worked as an independent predictive factor for OS in both univariate and multivariate Cox regression analyses (HR> 1, P< 0.001). Additionally, by RT-qPCR, we confirmed that NSCLC cell lines have higher levels of the three adverse prognostic NETs-related lncRNAs than normal lung cells. The expression of lncRNAs significantly increases after NETs stimulation. In short, the 12 NETs-related lncRNAs and their model could play effective roles as molecular markers in predicting survival for NSCLC patients.
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Markou AN, Smilkou S, Tsaroucha E, Lianidou E. The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1. Diagnostics (Basel) 2021; 11:1160. [PMID: 34202021 DOI: 10.3390/diagnostics11071160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/24/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
The presence of contaminating gDNA in RNA preparations is a frequent cause of false positives in RT-PCR-based analysis. However, in some cases, this cannot be avoided, especially when there are no exons-intron junctions in the lncRNA sequences. Due to the lack of exons in few of long noncoding RNAs (lncRNAs) and the lack of DNAse treatment step in most studies reported so far, serious questions are raised about the specificity of lncRNA detection and the potential of reporting false-positive results. We hypothesized that minute amounts of gDNA usually co-extracted with RNA could give false-positive signals since primers would specifically bind to gDNA due to the lack of junction. In the current study, we evaluated the effect of gDNA and other forms of DNA like extrachromosomal circular DNAs (eccDNAs) contamination and the importance of including a DNAse treatment step on lncRNAsexpression.As a model, we have chosen as one of the most widely studied lncRNAs in cancer namely MALAT1, which lacks exons. When we tested this hypothesis in plasma and primary tissue samples from NSCLC patients, our findings clearly indicated that results on MALAT1 expression are highly affected by the presence of DNA contamination and that the DNAse treatment step is absolutely necessary to avoid false positive results.
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Xu L, Liu W, Li T, Hu Y, Wang Y, Huang L, Wang Y, Shao S, Liu X, Zhan Q. Long non-coding RNA SMASR inhibits the EMT by negatively regulating TGF-β/Smad signaling pathway in lung cancer. Oncogene 2021; 40:3578-92. [PMID: 33931741 DOI: 10.1038/s41388-021-01760-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022]
Abstract
TGF-β/Smad signaling pathway plays an important role in EMT during cancer progression. Long non-coding RNAs (lncRNAs) are involved in various behaviors of cancer cells, including EMT. Here, we report a novel lncRNA adjacent to Smad3, named Smad3-associated long non-coding RNA (SMASR). SMASR is downregulated by TGF-β via Smad2/3 in lung cancer cells. Knockdown of SMASR induces EMT and increases the migration and invasion of lung cancer cells. Moreover, knockdown of SMASR promotes the phosphorylation of Smad2/3. Mechanistically, SMASR interacts with Smad2/3 and inhibits the expression of TGFBR1, the TGF-β type I receptor responsible for phosphorylation of Smad2/3, thus leading to inactivation of TGF-β/Smad signaling pathway. Clinically, SMASR is downregulated in lung cancer tissues. Collectively, our findings prove a critical role of SMASR in EMT of lung cancer by forming a negative feedback loop with TGF-β/Smad signaling pathway.
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Che H, Che Y, Zhang Z, Lu Q. Long Non-Coding RNA LINC01929 Accelerates Progression of Oral Squamous Cell Carcinoma by Targeting the miR-137-3p/FOXC1 Axis. Front Oncol 2021; 11:657876. [PMID: 33968763 PMCID: PMC8097103 DOI: 10.3389/fonc.2021.657876] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, additional long noncoding RNAs (lncRNAs) have been identified and their possible roles were investigated in a variety of human tumors. One of these lncRNAs, LINC01929, promoted the progression of some cancers, whereas its expression and biological function in human oral squamous cell carcinoma (OSCC) remains still mostly uncertain. The LINC01929 expression in OSCC tissues or cell lines was identified via quantitative real-time polymerase chain reaction. The cell counting kit-8, transwell migration, wound-healing, and flow cytometry assays were utilized to characterize the functions of LINC01929 in OSCC cells. The interactive relationships between LINC01929 and miR-137-3p, miR-137-3p and Forkhead box C1 (FOXC1) were investigated by the dual-luciferase activity assay. Our findings demonstrated that LINC01929 was highly expressed in OSCC tissue samples and cell lines, whereas miR-137-3p expression was downregulated. LINC01929 acted as a carcinogenic lncRNA with accelerated OSCC cell proliferation, migration and invasion, and suppression of apoptosis. We further indicated that LINC01929 facilitated tumor growth in xenograft mouse models. Mechanistically, LINC01929 acted as a sponge for miR-137-3p to elevate FOXC1 expression, which is the target of miR-137-3p. In addition, downregulated miR-137-3p expression rescued the suppressive behaviors of LINC01929 knockdown on the biological behaviors of OSCC cells. Taken together, LINC01929 functioned as a tumor-promoting lncRNA via the miR-137-3p/FOXC1 axis in OSCC, suggesting novel targets for OSCC therapy.
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Affiliation(s)
- Hongze Che
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Yanhai Che
- Department of Science and Education, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhimin Zhang
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Qing Lu
- Department of General Dentistry, Hospital of Stomatology, Jilin University, Changchun, China
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Wang X, Sun H, Hu Z, Mei P, Wu Y, Zhu M. NUTM2A-AS1 silencing alleviates LPS-induced apoptosis and inflammation in dental pulp cells through targeting let-7c-5p/HMGB1 axis. Int Immunopharmacol 2021; 96:107497. [PMID: 33831808 DOI: 10.1016/j.intimp.2021.107497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Long non-coding RNA (lncRNA) NUTM2A antisense RNA 1 (NUTM2A-AS1) has been reported to be abnormally up-regulated in pulpitis tissues. However, the function of NUTM2A-AS1 in pulpitis remains unclear. The aim of this study was to investigate the role and working mechanism of NUTM2A-AS1 in pulpitis using lipopolysaccharide (LPS)-treated human dental pulp cells (HDPCs). METHODS 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometry and lactate dehydrogenase (LDH) release detection assay were conducted to analyze the viability of HDPCs. Cell inflammatory response was analyzed through measuring the protein levels of interleukin-6 (IL-6) and IL-8. Western blot assay and quantitative real-time polymerase chain reaction (qRT-PCR) were applied to measure protein expression and RNA expression, respectively. Bioinformatic database StarBase was used to predict the possible targets of NUTM2A-AS1 and let-7c-5p, and dual-luciferase reporter assay was conducted to verify these intermolecular interactions. RESULTS LPS stimulation restrained cell viability and induced cell apoptosis and inflammation of HDPCs. LPS exposure up-regulated the expression of NUTM2A-AS1 and High-Mobility Group Box 1 (HMGB1) and down-regulated the level of let-7c-5p. LPS-induced injury in HDPCs was partly attenuated by the silencing of NUTM2A-AS1 or HMGB1. Let-7c-5p was confirmed as a direct target of NUTM2A-AS1, and let-7c-5p bound to the 3' untranslated region (3'UTR) of HMGB1 messenger RNA (mRNA) in HDPCs. HMGB1 overexpression largely overturned NUTM2A-AS1 silencing-mediated effects in LPS-induced HDPCs. CONCLUSION NUTM2A-AS1 knockdown attenuated LPS-induced damage in HDPCs partly through targeting let-7c-5p/HMGB1 axis.
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Affiliation(s)
- Xuechun Wang
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Huijun Sun
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Zhekai Hu
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Peng Mei
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Yanqi Wu
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China
| | - Min Zhu
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai 200011, China.
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Fan F, Huang Z, Chen Y. Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis. PeerJ 2021; 9:e11018. [PMID: 33732554 PMCID: PMC7950217 DOI: 10.7717/peerj.11018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/06/2021] [Indexed: 12/16/2022] Open
Abstract
Background Psoriasis is a chronic immune-mediated inflammatory dermatosis. Long noncoding RNAs (lncRNAs) play an important role in immune-related diseases. This study aimed to identify potential immune-related lncRNA biomarkers for psoriasis. Methods We screened differentially expressed immune-related lncRNAs biomarkers using GSE13355 (skin biopsy samples of 180 cases) from Gene Expression Omnibus (GEO). Moreover, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) were performed to explore biological mechanisms in psoriasis. In addition, we performed LASSO logistic regression to identify potential diagnostic lncRNAs and further verify the diagnostic value and relationship with drug response using two validation sets: GSE30999 (skin biopsy samples of 170 cases) and GSE106992 (skin biopsy samples of 192 cases). Furthermore, we estimated the degree of infiltrated immune cells and investigated the correlation between infiltrated immune cells and diagnostic lncRNA biomarkers. Results A total of 394 differentially expressed genes (DEGs) were extracted from gene expression profile. GO and KEGG analysis of target genes found that immune-related lncRNAs were primarily associated with epidermis development, skin development, collagen-containing extracellular matrix, and glycosaminoglycan binding and mainly enriched in cytokine-cytokine receptor interaction and influenza A and chemokine signaling pathway. We found that LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1, CARMN, CCDC18-AS1, EPB41L4A-AS, and LINC01214 exhibited well diagnostic efficacy. The ROC and ROC CI were 0.944 (0.907–0.982), 0.953 (0.919–0.987), 0.822 (0.758–0.887), 0.854 (0.797–0.911), 0.957(0.929–0.985), 0.894 (0.846–0.942), and 0.964 (0.937–0.991) for LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1,CARMN, CCDC18-AS1, EPB41L4A-AS1, and LINC01214. LINC01137, LINC01215, and LINC01214 were correlated with drug response. LINC01137, CCDC18-AS1, and CARMN were positively correlated with activated memory CD4 T cell, activated myeloid dendritic cell (DC), neutrophils, macrophage M1, and T follicular helper (Tfh) cells, while negatively correlated with T regulatory cell (Treg). LINC01215, MAPKAPK5-AS1, TPT1-AS1, EPB41L4A-AS, and LINC01214 were negatively correlated with activated memory CD4 T cell, activated myeloid DC, neutrophils, macrophage M1, and Tfh, while positively correlated with Treg. Conclusions These findings indicated that these immune-related lncRNAs may be used as potential diagnostic and predictive biomarkers for psoriasis.
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Affiliation(s)
- Feixiang Fan
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Dermatology, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Zhen Huang
- Department of Dermatology, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yongfeng Chen
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
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